9/22/2016,23:37:57.889,Running Canvas Somatic-WGS 1.11.0
9/22/2016,23:37:57.895,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test
9/22/2016,23:37:58.360,Running checkpoint 2: 'CanvasBin'
9/22/2016,23:37:58.410,Running checkpoint 1: 'CanvasSNV'
9/22/2016,23:37:58.437,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:37:58.437,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:37:58.437,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:37:58.437,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:37:58.437,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:37:58.437,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:37:58.437,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:37:58.438,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:37:58.438,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:37:58.438,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:37:58.438,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:37:58.438,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:37:58.438,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:37:58.438,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:37:58.440,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:37:58.440,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:37:58.440,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:37:58.440,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:37:58.440,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:37:58.441,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:37:58.441,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:37:58.441,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:37:58.442,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:37:58.442,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:37:58.671,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:37:58.671,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:37:58.673,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:37:58.674,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:37:58.674,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:37:58.674,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:37:58.674,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:37:58.674,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:37:58.674,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:37:58.674,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:37:58.675,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:37:58.675,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:37:58.690,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:37:58.690,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:37:58.690,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:37:58.691,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:37:58.691,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:37:58.698,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:37:58.698,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:37:58.698,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:37:58.698,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:37:58.710,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:37:58.715,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:37:58.719,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:37:58.720,Max job memory (GB): 0.3
9/22/2016,23:37:58.720,Longest job runtime (Hours): 0.00
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:37:58.808,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:37:58.809,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:37:58.810,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:39:41.784,Running Canvas Somatic-WGS 1.11.0
9/22/2016,23:39:41.790,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test
9/22/2016,23:39:41.899,Running checkpoint 2: 'CanvasBin'
9/22/2016,23:39:41.923,Running checkpoint 1: 'CanvasSNV'
9/22/2016,23:39:41.956,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:39:41.956,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:39:41.956,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:39:41.957,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:39:41.958,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:39:41.958,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:39:41.958,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:39:41.958,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:39:41.959,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:39:41.959,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:39:41.960,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:39:41.960,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:39:41.960,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:39:41.960,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:39:42.192,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:39:42.192,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:39:42.192,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:39:42.192,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:39:42.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:39:42.195,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:39:42.195,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:39:42.198,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:39:42.200,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:39:42.206,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:39:42.206,Max job memory (GB): 0.3
9/22/2016,23:39:42.206,Longest job runtime (Hours): 0.00
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:39:42.287,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:39:42.288,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:40:20.993,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:40:21.206,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:40:21.371,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:40:22.618,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:40:23.818,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:40:23.824,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:40:24.036,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:40:24.879,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:40:24.913,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:40:25.243,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:40:25.767,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:40:26.049,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:40:26.068,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:40:26.504,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:40:26.978,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:40:27.894,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:40:28.411,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:40:28.411,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:40:28.954,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:40:29.268,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:40:31.541,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:40:31.869,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:40:34.152,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:40:34.748,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:40:34.748,Max job memory (GB): 5.6
9/22/2016,23:40:34.748,Longest job runtime (Hours): 0.01
9/22/2016,23:41:08.176,Running Canvas Somatic-WGS 1.11.0
9/22/2016,23:41:08.182,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test[B
9/22/2016,23:41:08.293,Running checkpoint 2: 'CanvasBin'
9/22/2016,23:41:08.298,Running checkpoint 1: 'CanvasSNV'
9/22/2016,23:41:08.323,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr7-test[B.SNV.txt.gz
9/22/2016,23:41:08.323,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr4-test[B.SNV.txt.gz
9/22/2016,23:41:08.323,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr8-test[B.SNV.txt.gz
9/22/2016,23:41:08.323,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr5-test[B.SNV.txt.gz
9/22/2016,23:41:08.323,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr20-test[B.SNV.txt.gz
9/22/2016,23:41:08.324,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr2-test[B.SNV.txt.gz
9/22/2016,23:41:08.324,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr19-test[B.SNV.txt.gz
9/22/2016,23:41:08.324,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr21-test[B.SNV.txt.gz
9/22/2016,23:41:08.324,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr1-test[B.SNV.txt.gz
9/22/2016,23:41:08.324,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr3-test[B.SNV.txt.gz
9/22/2016,23:41:08.324,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr10-test[B.SNV.txt.gz
9/22/2016,23:41:08.325,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr22-test[B.SNV.txt.gz
9/22/2016,23:41:08.326,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr12-test[B.SNV.txt.gz
9/22/2016,23:41:08.326,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr6-test[B.SNV.txt.gz
9/22/2016,23:41:08.326,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr13-test[B.SNV.txt.gz
9/22/2016,23:41:08.327,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chrX-test[B.SNV.txt.gz
9/22/2016,23:41:08.327,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chrY-test[B.SNV.txt.gz
9/22/2016,23:41:08.327,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr9-test[B.SNV.txt.gz
9/22/2016,23:41:08.328,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr15-test[B.SNV.txt.gz
9/22/2016,23:41:08.328,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr11-test[B.SNV.txt.gz
9/22/2016,23:41:08.328,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr17-test[B.SNV.txt.gz
9/22/2016,23:41:08.328,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr16-test[B.SNV.txt.gz
9/22/2016,23:41:08.328,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr18-test[B.SNV.txt.gz
9/22/2016,23:41:08.329,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr14-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr8-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr10-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr5-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr2-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr19-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr1-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr3-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr6-test[B.SNV.txt.gz
9/22/2016,23:41:08.507,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr7-test[B.SNV.txt.gz
9/22/2016,23:41:08.508,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr14-test[B.SNV.txt.gz
9/22/2016,23:41:08.519,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr4-test[B.SNV.txt.gz
9/22/2016,23:41:08.519,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr11-test[B.SNV.txt.gz
9/22/2016,23:41:08.521,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr15-test[B.SNV.txt.gz
9/22/2016,23:41:08.527,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr17-test[B.SNV.txt.gz
9/22/2016,23:41:08.530,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr13-test[B.SNV.txt.gz
9/22/2016,23:41:08.544,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr18-test[B.SNV.txt.gz
9/22/2016,23:41:08.544,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr12-test[B.SNV.txt.gz
9/22/2016,23:41:08.551,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr22-test[B.SNV.txt.gz
9/22/2016,23:41:08.551,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr20-test[B.SNV.txt.gz
9/22/2016,23:41:08.555,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chrY-test[B.SNV.txt.gz
9/22/2016,23:41:08.555,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chrX-test[B.SNV.txt.gz
9/22/2016,23:41:08.564,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr21-test[B.SNV.txt.gz
9/22/2016,23:41:08.564,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr16-test[B.SNV.txt.gz
9/22/2016,23:41:08.564,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/chr9-test[B.SNV.txt.gz
9/22/2016,23:41:08.565,Max job memory (GB): 4.0
9/22/2016,23:41:08.565,Longest job runtime (Hours): 0.00
9/22/2016,23:41:08.658,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr1.dat" 
9/22/2016,23:41:08.658,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr2.dat" 
9/22/2016,23:41:08.658,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr3.dat" 
9/22/2016,23:41:08.658,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr4.dat" 
9/22/2016,23:41:08.658,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr5.dat" 
9/22/2016,23:41:08.658,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr6.dat" 
9/22/2016,23:41:08.658,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr7.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chrX.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr8.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr9.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr10.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr11.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr12.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr13.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr14.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr15.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr16.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr17.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr18.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr20.dat" 
9/22/2016,23:41:08.659,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chrY.dat" 
9/22/2016,23:41:08.660,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr19.dat" 
9/22/2016,23:41:08.660,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr22.dat" 
9/22/2016,23:41:08.660,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test[B/test[B_0_chr21.dat" 
9/22/2016,23:41:19.926,Running Canvas Somatic-WGS 1.11.0
9/22/2016,23:41:19.932,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test
9/22/2016,23:41:20.052,Running checkpoint 2: 'CanvasBin'
9/22/2016,23:41:20.057,Running checkpoint 1: 'CanvasSNV'
9/22/2016,23:41:20.085,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:41:20.085,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:41:20.085,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:41:20.085,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:41:20.085,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:41:20.085,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:41:20.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:41:20.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:41:20.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:41:20.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:41:20.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:41:20.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:41:20.087,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:41:20.087,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:41:20.087,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:41:20.087,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:41:20.087,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:41:20.088,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:41:20.088,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:41:20.089,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:41:20.089,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:41:20.089,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:41:20.089,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:41:20.090,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:41:20.262,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:41:20.263,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:41:20.285,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:41:20.285,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:41:20.285,Max job memory (GB): 0.3
9/22/2016,23:41:20.286,Longest job runtime (Hours): 0.00
9/22/2016,23:41:20.354,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:41:20.355,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:41:20.356,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:41:59.074,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:41:59.186,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:41:59.193,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:41:59.768,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:42:00.689,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:42:00.951,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:42:01.000,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:42:01.232,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:42:01.372,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:42:01.381,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:42:03.102,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:42:03.229,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:42:03.877,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:42:04.467,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:42:04.644,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:42:05.710,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:42:05.816,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:42:07.212,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:42:07.543,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:42:09.404,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:42:09.608,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:42:10.505,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:42:12.311,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:42:14.502,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:42:14.502,Max job memory (GB): 5.5
9/22/2016,23:42:14.502,Longest job runtime (Hours): 0.02
9/22/2016,23:47:22.806,Running Canvas Somatic-WGS 1.11.0
9/22/2016,23:47:22.818,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test
9/22/2016,23:47:23.045,Running checkpoint 2: 'CanvasBin'
9/22/2016,23:47:23.049,Running checkpoint 1: 'CanvasSNV'
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:47:23.081,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:47:23.082,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:47:23.082,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:47:23.082,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:47:23.082,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:47:23.082,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:47:23.083,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:47:23.083,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:47:23.084,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:47:23.084,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:47:23.084,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:47:23.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:47:23.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:47:23.086,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:47:23.294,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:47:23.295,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:47:23.295,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:47:23.295,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:47:23.295,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:47:23.295,Max job memory (GB): 0.3
9/22/2016,23:47:23.295,Longest job runtime (Hours): 0.00
9/22/2016,23:47:23.421,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:47:23.422,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:47:23.423,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:47:23.424,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:47:23.424,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:47:23.424,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:47:53.255,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:47:53.255,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:47:53.255,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:47:53.255,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:47:53.255,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:47:53.276,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:47:53.276,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:47:53.284,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:47:53.307,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:47:53.378,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:47:53.378,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:47:53.380,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:47:53.476,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:47:53.485,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:47:53.486,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:47:53.547,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:47:53.641,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:47:53.667,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:47:53.667,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:47:53.667,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:47:53.701,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:47:53.701,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:47:53.762,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:47:53.967,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:47:53.967,Max job memory (GB): 6.0
9/22/2016,23:47:53.968,Longest job runtime (Hours): 0.01
9/22/2016,23:53:21.042,Running Canvas Somatic-WGS 1.11.0
9/22/2016,23:53:21.052,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test
9/22/2016,23:53:21.238,Running checkpoint 2: 'CanvasBin'
9/22/2016,23:53:21.296,Running checkpoint 1: 'CanvasSNV'
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:53:21.336,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:53:21.337,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:53:21.339,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:53:21.339,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:53:21.516,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/22/2016,23:53:21.517,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/22/2016,23:53:21.517,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/22/2016,23:53:21.528,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/22/2016,23:53:21.556,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/22/2016,23:53:21.556,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/22/2016,23:53:21.556,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/22/2016,23:53:21.556,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/22/2016,23:53:21.556,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/22/2016,23:53:21.557,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/22/2016,23:53:21.562,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/22/2016,23:53:21.563,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/22/2016,23:53:21.564,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/22/2016,23:53:21.572,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/22/2016,23:53:21.572,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/22/2016,23:53:21.573,Max job memory (GB): 0.3
9/22/2016,23:53:21.573,Longest job runtime (Hours): 0.00
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:53:21.634,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:53:21.635,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:53:21.636,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:53:21.636,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:53:51.290,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/22/2016,23:53:51.387,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/22/2016,23:53:51.388,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/22/2016,23:53:51.439,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/22/2016,23:53:51.456,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/22/2016,23:53:51.457,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/22/2016,23:53:51.497,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/22/2016,23:53:51.568,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/22/2016,23:53:51.581,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/22/2016,23:53:51.583,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/22/2016,23:53:51.583,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/22/2016,23:53:51.583,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/22/2016,23:53:51.589,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/22/2016,23:53:51.589,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/22/2016,23:53:51.589,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/22/2016,23:53:51.589,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/22/2016,23:53:51.589,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/22/2016,23:53:51.594,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/22/2016,23:53:51.800,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/22/2016,23:53:51.809,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/22/2016,23:53:51.838,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/22/2016,23:53:51.871,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/22/2016,23:53:51.888,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/22/2016,23:53:52.786,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/22/2016,23:53:52.786,Max job memory (GB): 5.7
9/22/2016,23:53:52.786,Longest job runtime (Hours): 0.01
9/23/2016,15:39:52.315,Running Canvas Somatic-WGS 1.11.0
9/23/2016,15:39:52.326,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test
9/23/2016,15:39:52.511,Running checkpoint 2: 'CanvasBin'
9/23/2016,15:39:52.530,Running checkpoint 1: 'CanvasSNV'
9/23/2016,15:39:52.569,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/23/2016,15:39:52.570,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/23/2016,15:39:52.570,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/23/2016,15:39:52.570,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/23/2016,15:39:52.571,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/23/2016,15:39:52.571,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/23/2016,15:39:52.571,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/23/2016,15:39:52.571,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/23/2016,15:39:52.571,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/23/2016,15:39:52.572,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/23/2016,15:39:52.573,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/23/2016,15:39:52.575,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/23/2016,15:39:52.575,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/23/2016,15:39:52.576,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/23/2016,15:39:52.888,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/23/2016,15:39:52.888,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/23/2016,15:39:52.888,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/23/2016,15:39:52.899,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/23/2016,15:39:52.899,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/23/2016,15:39:52.899,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/23/2016,15:39:52.901,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/23/2016,15:39:52.901,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/23/2016,15:39:52.921,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/23/2016,15:39:52.921,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/23/2016,15:39:52.921,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/23/2016,15:39:52.921,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/23/2016,15:39:52.933,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/23/2016,15:39:52.933,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/23/2016,15:39:52.933,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/23/2016,15:39:52.933,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/23/2016,15:39:52.933,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/23/2016,15:39:52.934,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/23/2016,15:39:52.934,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/23/2016,15:39:52.934,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/23/2016,15:39:52.934,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/23/2016,15:39:52.934,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/23/2016,15:39:52.934,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/23/2016,15:39:52.938,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/23/2016,15:39:52.938,Max job memory (GB): 0.3
9/23/2016,15:39:52.938,Longest job runtime (Hours): 0.00
9/23/2016,15:39:53.009,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/23/2016,15:39:53.009,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/23/2016,15:39:53.009,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/23/2016,15:39:53.009,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/23/2016,15:39:53.009,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/23/2016,15:39:53.009,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/23/2016,15:39:53.009,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/23/2016,15:39:53.010,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/23/2016,15:39:53.011,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/23/2016,15:39:53.011,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/23/2016,15:39:53.011,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/23/2016,15:39:53.011,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/23/2016,15:39:53.011,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/23/2016,15:40:22.675,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/23/2016,15:40:22.710,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/23/2016,15:40:22.711,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/23/2016,15:40:22.711,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/23/2016,15:40:22.711,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/23/2016,15:40:22.712,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/23/2016,15:40:22.712,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/23/2016,15:40:22.740,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/23/2016,15:40:22.789,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/23/2016,15:40:22.860,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/23/2016,15:40:22.873,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/23/2016,15:40:22.874,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/23/2016,15:40:22.874,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/23/2016,15:40:22.876,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/23/2016,15:40:22.880,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/23/2016,15:40:22.880,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/23/2016,15:40:22.880,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/23/2016,15:40:22.881,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/23/2016,15:40:22.881,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/23/2016,15:40:22.881,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/23/2016,15:40:23.043,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/23/2016,15:40:23.047,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/23/2016,15:40:23.049,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/23/2016,15:40:23.050,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/23/2016,15:40:23.050,Max job memory (GB): 6.2
9/23/2016,15:40:23.050,Longest job runtime (Hours): 0.01
9/23/2016,15:45:05.801,Running Canvas Somatic-WGS 1.11.0
9/23/2016,15:45:05.811,Command-line arguments: Somatic-WGS -b ../all_sorted_rmdup_sorted.bam --b-allele-vcf snp_ab.vcf -o ./ -r /home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna -g /home/rajeha/WholeGenomeFasta -f filter.bed -n test
9/23/2016,15:45:06.007,Running checkpoint 2: 'CanvasBin'
9/23/2016,15:45:06.066,Running checkpoint 1: 'CanvasSNV'
9/23/2016,15:45:06.103,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/23/2016,15:45:06.103,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/23/2016,15:45:06.104,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/23/2016,15:45:06.104,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/23/2016,15:45:06.104,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/23/2016,15:45:06.104,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/23/2016,15:45:06.105,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/23/2016,15:45:06.105,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/23/2016,15:45:06.105,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/23/2016,15:45:06.105,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/23/2016,15:45:06.105,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/23/2016,15:45:06.105,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/23/2016,15:45:06.106,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/23/2016,15:45:06.106,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/23/2016,15:45:06.106,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/23/2016,15:45:06.106,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/23/2016,15:45:06.106,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/23/2016,15:45:06.106,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/23/2016,15:45:06.107,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/23/2016,15:45:06.107,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/23/2016,15:45:06.108,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/23/2016,15:45:06.108,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/23/2016,15:45:06.108,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/23/2016,15:45:06.110,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/23/2016,15:45:06.281,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr21 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr21-test.SNV.txt.gz
9/23/2016,15:45:06.281,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr14 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr14-test.SNV.txt.gz
9/23/2016,15:45:06.281,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr10 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr10-test.SNV.txt.gz
9/23/2016,15:45:06.281,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr13 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr13-test.SNV.txt.gz
9/23/2016,15:45:06.281,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr11 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr11-test.SNV.txt.gz
9/23/2016,15:45:06.281,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr22 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr22-test.SNV.txt.gz
9/23/2016,15:45:06.281,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrX /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrX-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr4 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr4-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr5 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr5-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr1 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr1-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr3 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr3-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr9 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr9-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr7 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr7-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr8 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr8-test.SNV.txt.gz
9/23/2016,15:45:06.291,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr16 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr16-test.SNV.txt.gz
9/23/2016,15:45:06.299,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr6 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr6-test.SNV.txt.gz
9/23/2016,15:45:06.300,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr17 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr17-test.SNV.txt.gz
9/23/2016,15:45:06.301,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr18 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr18-test.SNV.txt.gz
9/23/2016,15:45:06.319,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr15 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr15-test.SNV.txt.gz
9/23/2016,15:45:06.319,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr20 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr20-test.SNV.txt.gz
9/23/2016,15:45:06.320,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr19 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr19-test.SNV.txt.gz
9/23/2016,15:45:06.320,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr12 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr12-test.SNV.txt.gz
9/23/2016,15:45:06.320,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chrY /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chrY-test.SNV.txt.gz
9/23/2016,15:45:06.337,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasSNV.exe chr2 /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/snp_ab.vcf /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam /mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/chr2-test.SNV.txt.gz
9/23/2016,15:45:06.337,Max job memory (GB): 0.3
9/23/2016,15:45:06.337,Longest job runtime (Hours): 0.00
9/23/2016,15:45:06.397,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/23/2016,15:45:06.397,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/23/2016,15:45:06.397,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/23/2016,15:45:06.397,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/23/2016,15:45:06.398,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/23/2016,15:45:06.399,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/23/2016,15:45:06.400,Launch process: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/23/2016,15:45:36.070,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr3 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr3.dat" 
9/23/2016,15:45:36.096,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr7 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr7.dat" 
9/23/2016,15:45:36.124,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrY -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrY.dat" 
9/23/2016,15:45:36.124,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr8 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr8.dat" 
9/23/2016,15:45:36.206,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr16 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr16.dat" 
9/23/2016,15:45:36.256,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr20 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr20.dat" 
9/23/2016,15:45:36.270,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr17 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr17.dat" 
9/23/2016,15:45:36.270,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr21 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr21.dat" 
9/23/2016,15:45:36.270,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr14 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr14.dat" 
9/23/2016,15:45:36.270,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr12 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr12.dat" 
9/23/2016,15:45:36.270,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr19 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr19.dat" 
9/23/2016,15:45:36.270,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr5 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr5.dat" 
9/23/2016,15:45:36.278,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr22 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr22.dat" 
9/23/2016,15:45:36.278,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr11 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr11.dat" 
9/23/2016,15:45:36.279,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr13 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr13.dat" 
9/23/2016,15:45:36.279,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr1 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr1.dat" 
9/23/2016,15:45:36.279,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr4 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr4.dat" 
9/23/2016,15:45:36.307,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr2 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr2.dat" 
9/23/2016,15:45:36.439,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr15 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr15.dat" 
9/23/2016,15:45:36.459,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chrX -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chrX.dat" 
9/23/2016,15:45:36.524,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr18 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr18.dat" 
9/23/2016,15:45:36.550,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr6 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr6.dat" 
9/23/2016,15:45:36.550,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr10 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr10.dat" 
9/23/2016,15:45:36.550,Process exited with code 1: /home/rajeha/bin/mono-4.6.0/bin/mono /home/rajeha/bin/Canvas_1.11.0/CanvasBin.exe -b "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/all_sorted_rmdup_sorted.bam" -p -r "/home/rajeha/ref/GCA_000001405.15_GRCh38_genomic.fna" -c chr9 -m GCContentWeighted -f "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/filter.bed" -d 100 -o "/mnt/xfs/extra/Lionberger_1978_12345678/ACGCGGG/test_canvas/TempCNV_test/test_0_chr9.dat" 
9/23/2016,15:45:36.550,Max job memory (GB): 6.0
9/23/2016,15:45:36.550,Longest job runtime (Hours): 0.01