In test mode. Program data path: /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq ================================================================================ breseq 0.32.0 revision 6ff6de7d1b87 http://barricklab.org/breseq Active Developers: Barrick JE, Deatherage DE Contact: breseq is free software; you can redistribute it and/or modify it under the terms the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) any later version. Copyright (c) 2008-2010 Michigan State University Copyright (c) 2011-2017 The University of Texas at Austin If you use breseq in your research, please cite: Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151: 165–188. If you use structural variation (junction) predictions, please cite: Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C., Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. (2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15:1039. ================================================================================ ---> bowtie2 :: version 2.3.2 [/home/apps/software/Bowtie2/2.3.2-IGB-gcc-4.9.4/bin/bowtie2] ---> R :: version 3.4.2 [/home/apps/software/R/3.4.2-IGB-gcc-4.9.4/bin/R] +++ NOW PROCESSING Read and reference sequence file input READ FILE::G1841MIC_R1.trimAQ Converting/filtering FASTQ file... Original base quality format: SANGER New format: SANGER Original reads: 3754607 bases: 912641200 Filtered reads: none Analyzed reads: 3754607 bases: 912641200 READ FILE::G1841MIC_R2.trimAQ Converting/filtering FASTQ file... Original base quality format: SANGER New format: SANGER Original reads: 3754607 bases: 870350879 Filtered reads: 1 bases: 30 (≥90.0% same base) Analyzed reads: 3754606 bases: 870350849 ::TOTAL:: Original reads: 7509214 bases: 1782992079 Analyzed reads: 7509213 bases: 1782992049 [samtools] faidx G1841MIC/data/reference.fasta REFERENCE: NZ_JRYM01000009 LENGTH: 265399 REFERENCE: NZ_JRYM01000010 LENGTH: 30857 REFERENCE: NZ_JRYM01000011 LENGTH: 33412 REFERENCE: NZ_JRYM01000012 LENGTH: 61191 REFERENCE: NZ_JRYM01000013 LENGTH: 56950 REFERENCE: NZ_JRYM01000014 LENGTH: 114596 REFERENCE: NZ_JRYM01000015 LENGTH: 63522 REFERENCE: NZ_JRYM01000016 LENGTH: 3105 REFERENCE: NZ_JRYM01000017 LENGTH: 47400 REFERENCE: NZ_JRYM01000018 LENGTH: 102332 REFERENCE: NZ_JRYM01000001 LENGTH: 221437 REFERENCE: NZ_JRYM01000019 LENGTH: 178167 REFERENCE: NZ_JRYM01000020 LENGTH: 57854 REFERENCE: NZ_JRYM01000021 LENGTH: 63595 REFERENCE: NZ_JRYM01000022 LENGTH: 40792 REFERENCE: NZ_JRYM01000023 LENGTH: 109522 REFERENCE: NZ_JRYM01000024 LENGTH: 125735 REFERENCE: NZ_JRYM01000025 LENGTH: 258417 REFERENCE: NZ_JRYM01000026 LENGTH: 94970 REFERENCE: NZ_JRYM01000027 LENGTH: 38491 REFERENCE: NZ_JRYM01000028 LENGTH: 10840 REFERENCE: NZ_JRYM01000002 LENGTH: 78538 REFERENCE: NZ_JRYM01000029 LENGTH: 31516 REFERENCE: NZ_JRYM01000030 LENGTH: 3110 REFERENCE: NZ_JRYM01000031 LENGTH: 132940 REFERENCE: NZ_JRYM01000032 LENGTH: 224090 REFERENCE: NZ_JRYM01000033 LENGTH: 29384 REFERENCE: NZ_JRYM01000034 LENGTH: 112432 REFERENCE: NZ_JRYM01000035 LENGTH: 29709 REFERENCE: NZ_JRYM01000036 LENGTH: 29247 REFERENCE: NZ_JRYM01000037 LENGTH: 35348 REFERENCE: NZ_JRYM01000038 LENGTH: 88265 REFERENCE: NZ_JRYM01000003 LENGTH: 132511 REFERENCE: NZ_JRYM01000039 LENGTH: 13210 REFERENCE: NZ_JRYM01000040 LENGTH: 54995 REFERENCE: NZ_JRYM01000041 LENGTH: 139987 REFERENCE: NZ_JRYM01000042 LENGTH: 33606 REFERENCE: NZ_JRYM01000043 LENGTH: 155514 REFERENCE: NZ_JRYM01000044 LENGTH: 60376 REFERENCE: NZ_JRYM01000045 LENGTH: 15864 REFERENCE: NZ_JRYM01000046 LENGTH: 41512 REFERENCE: NZ_JRYM01000047 LENGTH: 55007 REFERENCE: NZ_JRYM01000048 LENGTH: 1684 REFERENCE: NZ_JRYM01000049 LENGTH: 2976 REFERENCE: NZ_JRYM01000050 LENGTH: 4631 REFERENCE: NZ_JRYM01000051 LENGTH: 7990 REFERENCE: NZ_JRYM01000052 LENGTH: 1123 REFERENCE: NZ_JRYM01000053 LENGTH: 8559 REFERENCE: NZ_JRYM01000054 LENGTH: 7957 REFERENCE: NZ_JRYM01000055 LENGTH: 2389 REFERENCE: NZ_JRYM01000056 LENGTH: 32723 REFERENCE: NZ_JRYM01000057 LENGTH: 39149 REFERENCE: NZ_JRYM01000058 LENGTH: 85495 REFERENCE: NZ_JRYM01000004 LENGTH: 353785 REFERENCE: NZ_JRYM01000059 LENGTH: 9159 REFERENCE: NZ_JRYM01000060 LENGTH: 31052 REFERENCE: NZ_JRYM01000061 LENGTH: 1258 REFERENCE: NZ_JRYM01000062 LENGTH: 754 REFERENCE: NZ_JRYM01000063 LENGTH: 1321 REFERENCE: NZ_JRYM01000064 LENGTH: 447 REFERENCE: NZ_JRYM01000065 LENGTH: 2704 REFERENCE: NZ_JRYM01000066 LENGTH: 1330 REFERENCE: NZ_JRYM01000067 LENGTH: 1829 REFERENCE: NZ_JRYM01000068 LENGTH: 3267 REFERENCE: NZ_JRYM01000005 LENGTH: 67265 REFERENCE: NZ_JRYM01000069 LENGTH: 706 REFERENCE: NZ_JRYM01000070 LENGTH: 734 REFERENCE: NZ_JRYM01000071 LENGTH: 1501 REFERENCE: NZ_JRYM01000072 LENGTH: 1343 REFERENCE: NZ_JRYM01000073 LENGTH: 766 REFERENCE: NZ_JRYM01000074 LENGTH: 1893 REFERENCE: NZ_JRYM01000075 LENGTH: 8912 REFERENCE: NZ_JRYM01000076 LENGTH: 445 REFERENCE: NZ_JRYM01000077 LENGTH: 2751 REFERENCE: NZ_JRYM01000078 LENGTH: 2073 REFERENCE: NZ_JRYM01000006 LENGTH: 935 REFERENCE: NZ_JRYM01000079 LENGTH: 550 REFERENCE: NZ_JRYM01000080 LENGTH: 875 REFERENCE: NZ_JRYM01000081 LENGTH: 1022 REFERENCE: NZ_JRYM01000082 LENGTH: 489 REFERENCE: NZ_JRYM01000083 LENGTH: 541 REFERENCE: NZ_JRYM01000084 LENGTH: 823 REFERENCE: NZ_JRYM01000085 LENGTH: 1475 REFERENCE: NZ_JRYM01000086 LENGTH: 1481 REFERENCE: NZ_JRYM01000087 LENGTH: 2970 REFERENCE: NZ_JRYM01000088 LENGTH: 671 REFERENCE: NZ_JRYM01000007 LENGTH: 176564 REFERENCE: NZ_JRYM01000089 LENGTH: 848 REFERENCE: NZ_JRYM01000008 LENGTH: 148236 +++ NOW PROCESSING Read alignment to reference genome [system] bowtie2-build -q G1841MIC/data/reference.fasta G1841MIC/02_reference_alignment/reference [system] bowtie2 -t -p 8 -L 31 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,1,0.9 -k 2000 --reorder -x G1841MIC/02_reference_alignment/reference -U G1841MIC/01_sequence_conversion/G1841MIC_R1.trimAQ.converted.fastq -S G1841MIC/02_reference_alignment/G1841MIC_R1.trimAQ.stage1.sam --un G1841MIC/02_reference_alignment/G1841MIC_R1.trimAQ.stage1.unmatched.fastq Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:49 3754607 reads; of these: 3754607 (100.00%) were unpaired; of these: 134313 (3.58%) aligned 0 times 3605875 (96.04%) aligned exactly 1 time 14419 (0.38%) aligned >1 times 96.42% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 [system] bowtie2 -t -p 8 -L 29 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,6,0.2 -k 2000 --reorder -x G1841MIC/02_reference_alignment/reference -U G1841MIC/02_reference_alignment/G1841MIC_R1.trimAQ.stage1.unmatched.fastq -S G1841MIC/02_reference_alignment/G1841MIC_R1.trimAQ.stage2.matched.sam Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:05 134313 reads; of these: 134313 (100.00%) were unpaired; of these: 96320 (71.71%) aligned 0 times 13173 (9.81%) aligned exactly 1 time 24820 (18.48%) aligned >1 times 28.29% overall alignment rate Time searching: 00:00:05 Overall time: 00:00:05 [system] bowtie2 -t -p 8 -L 31 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,1,0.9 -k 2000 --reorder -x G1841MIC/02_reference_alignment/reference -U G1841MIC/01_sequence_conversion/G1841MIC_R2.trimAQ.converted.fastq -S G1841MIC/02_reference_alignment/G1841MIC_R2.trimAQ.stage1.sam --un G1841MIC/02_reference_alignment/G1841MIC_R2.trimAQ.stage1.unmatched.fastq Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:47 3754606 reads; of these: 3754606 (100.00%) were unpaired; of these: 133629 (3.56%) aligned 0 times 3604068 (95.99%) aligned exactly 1 time 16909 (0.45%) aligned >1 times 96.44% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 [system] bowtie2 -t -p 8 -L 28 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,6,0.2 -k 2000 --reorder -x G1841MIC/02_reference_alignment/reference -U G1841MIC/02_reference_alignment/G1841MIC_R2.trimAQ.stage1.unmatched.fastq -S G1841MIC/02_reference_alignment/G1841MIC_R2.trimAQ.stage2.matched.sam Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:04 133629 reads; of these: 133629 (100.00%) were unpaired; of these: 96693 (72.36%) aligned 0 times 13291 (9.95%) aligned exactly 1 time 23645 (17.69%) aligned >1 times 27.64% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 [system] rm -f G1841MIC/02_reference_alignment/reference* [system] rm -f G1841MIC/02_reference_alignment/G1841MIC_R1.trimAQ.stage1.unmatched.fastq [system] rm -f G1841MIC/02_reference_alignment/G1841MIC_R1.trimAQ.stage1.sam [system] rm -f G1841MIC/02_reference_alignment/G1841MIC_R1.trimAQ.stage2.matched.sam [system] rm -f G1841MIC/02_reference_alignment/G1841MIC_R2.trimAQ.stage1.unmatched.fastq [system] rm -f G1841MIC/02_reference_alignment/G1841MIC_R2.trimAQ.stage1.sam [system] rm -f G1841MIC/02_reference_alignment/G1841MIC_R2.trimAQ.stage2.matched.sam +++ NOW PROCESSING Preprocessing alignments for candidate junction identification Preprocessing alignments. READ FILE::G1841MIC_R1.trimAQ ALIGNED READ:100000 ALIGNED READ:200000 ALIGNED READ:300000 ALIGNED READ:400000 ALIGNED READ:500000 ALIGNED READ:600000 ALIGNED READ:700000 ALIGNED READ:800000 ALIGNED READ:900000 ALIGNED READ:1000000 ALIGNED READ:1100000 ALIGNED READ:1200000 ALIGNED READ:1300000 ALIGNED READ:1400000 ALIGNED READ:1500000 ALIGNED READ:1600000 ALIGNED READ:1700000 ALIGNED READ:1800000 ALIGNED READ:1900000 ALIGNED READ:2000000 ALIGNED READ:2100000 ALIGNED READ:2200000 ALIGNED READ:2300000 ALIGNED READ:2400000 ALIGNED READ:2500000 ALIGNED READ:2600000 ALIGNED READ:2700000 ALIGNED READ:2800000 ALIGNED READ:2900000 ALIGNED READ:3000000 ALIGNED READ:3100000 ALIGNED READ:3200000 ALIGNED READ:3300000 ALIGNED READ:3400000 ALIGNED READ:3500000 ALIGNED READ:3600000 READ FILE::G1841MIC_R2.trimAQ ALIGNED READ:3700000 ALIGNED READ:3800000 ALIGNED READ:3900000 ALIGNED READ:4000000 ALIGNED READ:4100000 ALIGNED READ:4200000 ALIGNED READ:4300000 ALIGNED READ:4400000 ALIGNED READ:4500000 ALIGNED READ:4600000 ALIGNED READ:4700000 ALIGNED READ:4800000 ALIGNED READ:4900000 ALIGNED READ:5000000 ALIGNED READ:5100000 ALIGNED READ:5200000 ALIGNED READ:5300000 ALIGNED READ:5400000 ALIGNED READ:5500000 ALIGNED READ:5600000 ALIGNED READ:5700000 ALIGNED READ:5800000 ALIGNED READ:5900000 ALIGNED READ:6000000 ALIGNED READ:6100000 ALIGNED READ:6200000 ALIGNED READ:6300000 ALIGNED READ:6400000 ALIGNED READ:6500000 ALIGNED READ:6600000 ALIGNED READ:6700000 ALIGNED READ:6800000 ALIGNED READ:6900000 ALIGNED READ:7000000 ALIGNED READ:7100000 ALIGNED READ:7200000 ALIGNED READ:7300000 Summary... Aligned reads: 7316200 Read alignments: 7428776 Alignments split on indels: 2496 Reads with alignments split on indels: 2415 Split alignments: 123978 Reads with split alignments: 49726 +++ NOW PROCESSING Preliminary analysis of coverage distribution [samtools] import G1841MIC/data/reference.fasta.fai G1841MIC/03_candidate_junctions/best.sam G1841MIC/03_candidate_junctions/best.unsorted.bam [samtools] sort --threads 8 -o G1841MIC/03_candidate_junctions/best.bam -T G1841MIC/03_candidate_junctions/best.bam G1841MIC/03_candidate_junctions/best.unsorted.bam [samtools] index G1841MIC/03_candidate_junctions/best.bam G1841MIC/03_candidate_junctions/best.bam.bai REFERENCE: NZ_JRYM01000001 LENGTH: 221437 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 POSITION:160000 POSITION:170000 POSITION:180000 POSITION:190000 POSITION:200000 POSITION:210000 POSITION:220000 REFERENCE: NZ_JRYM01000002 LENGTH: 78538 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 REFERENCE: NZ_JRYM01000003 LENGTH: 132511 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 REFERENCE: NZ_JRYM01000004 LENGTH: 353785 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 POSITION:160000 POSITION:170000 POSITION:180000 POSITION:190000 POSITION:200000 POSITION:210000 POSITION:220000 POSITION:230000 POSITION:240000 POSITION:250000 POSITION:260000 POSITION:270000 POSITION:280000 POSITION:290000 POSITION:300000 POSITION:310000 POSITION:320000 POSITION:330000 POSITION:340000 POSITION:350000 REFERENCE: NZ_JRYM01000005 LENGTH: 67265 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 REFERENCE: NZ_JRYM01000006 LENGTH: 935 REFERENCE: NZ_JRYM01000007 LENGTH: 176564 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 POSITION:160000 POSITION:170000 REFERENCE: NZ_JRYM01000008 LENGTH: 148236 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 REFERENCE: NZ_JRYM01000009 LENGTH: 265399 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 POSITION:160000 POSITION:170000 POSITION:180000 POSITION:190000 POSITION:200000 POSITION:210000 POSITION:220000 POSITION:230000 POSITION:240000 POSITION:250000 POSITION:260000 REFERENCE: NZ_JRYM01000010 LENGTH: 30857 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000011 LENGTH: 33412 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000012 LENGTH: 61191 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 REFERENCE: NZ_JRYM01000013 LENGTH: 56950 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 REFERENCE: NZ_JRYM01000014 LENGTH: 114596 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 REFERENCE: NZ_JRYM01000015 LENGTH: 63522 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 REFERENCE: NZ_JRYM01000016 LENGTH: 3105 REFERENCE: NZ_JRYM01000017 LENGTH: 47400 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 REFERENCE: NZ_JRYM01000018 LENGTH: 102332 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 REFERENCE: NZ_JRYM01000019 LENGTH: 178167 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 POSITION:160000 POSITION:170000 REFERENCE: NZ_JRYM01000020 LENGTH: 57854 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 REFERENCE: NZ_JRYM01000021 LENGTH: 63595 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 REFERENCE: NZ_JRYM01000022 LENGTH: 40792 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 REFERENCE: NZ_JRYM01000023 LENGTH: 109522 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 REFERENCE: NZ_JRYM01000024 LENGTH: 125735 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 REFERENCE: NZ_JRYM01000025 LENGTH: 258417 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 POSITION:160000 POSITION:170000 POSITION:180000 POSITION:190000 POSITION:200000 POSITION:210000 POSITION:220000 POSITION:230000 POSITION:240000 POSITION:250000 REFERENCE: NZ_JRYM01000026 LENGTH: 94970 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 REFERENCE: NZ_JRYM01000027 LENGTH: 38491 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000028 LENGTH: 10840 POSITION:10000 REFERENCE: NZ_JRYM01000029 LENGTH: 31516 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000030 LENGTH: 3110 REFERENCE: NZ_JRYM01000031 LENGTH: 132940 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 REFERENCE: NZ_JRYM01000032 LENGTH: 224090 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 POSITION:160000 POSITION:170000 POSITION:180000 POSITION:190000 POSITION:200000 POSITION:210000 POSITION:220000 REFERENCE: NZ_JRYM01000033 LENGTH: 29384 POSITION:10000 POSITION:20000 REFERENCE: NZ_JRYM01000034 LENGTH: 112432 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 REFERENCE: NZ_JRYM01000035 LENGTH: 29709 POSITION:10000 POSITION:20000 REFERENCE: NZ_JRYM01000036 LENGTH: 29247 POSITION:10000 POSITION:20000 REFERENCE: NZ_JRYM01000037 LENGTH: 35348 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000038 LENGTH: 88265 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 REFERENCE: NZ_JRYM01000039 LENGTH: 13210 POSITION:10000 REFERENCE: NZ_JRYM01000040 LENGTH: 54995 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 REFERENCE: NZ_JRYM01000041 LENGTH: 139987 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 REFERENCE: NZ_JRYM01000042 LENGTH: 33606 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000043 LENGTH: 155514 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 POSITION:90000 POSITION:100000 POSITION:110000 POSITION:120000 POSITION:130000 POSITION:140000 POSITION:150000 REFERENCE: NZ_JRYM01000044 LENGTH: 60376 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 REFERENCE: NZ_JRYM01000045 LENGTH: 15864 POSITION:10000 REFERENCE: NZ_JRYM01000046 LENGTH: 41512 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 REFERENCE: NZ_JRYM01000047 LENGTH: 55007 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 REFERENCE: NZ_JRYM01000048 LENGTH: 1684 REFERENCE: NZ_JRYM01000049 LENGTH: 2976 REFERENCE: NZ_JRYM01000050 LENGTH: 4631 REFERENCE: NZ_JRYM01000051 LENGTH: 7990 REFERENCE: NZ_JRYM01000052 LENGTH: 1123 REFERENCE: NZ_JRYM01000053 LENGTH: 8559 REFERENCE: NZ_JRYM01000054 LENGTH: 7957 REFERENCE: NZ_JRYM01000055 LENGTH: 2389 REFERENCE: NZ_JRYM01000056 LENGTH: 32723 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000057 LENGTH: 39149 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000058 LENGTH: 85495 POSITION:10000 POSITION:20000 POSITION:30000 POSITION:40000 POSITION:50000 POSITION:60000 POSITION:70000 POSITION:80000 REFERENCE: NZ_JRYM01000059 LENGTH: 9159 REFERENCE: NZ_JRYM01000060 LENGTH: 31052 POSITION:10000 POSITION:20000 POSITION:30000 REFERENCE: NZ_JRYM01000061 LENGTH: 1258 REFERENCE: NZ_JRYM01000062 LENGTH: 754 REFERENCE: NZ_JRYM01000063 LENGTH: 1321 REFERENCE: NZ_JRYM01000064 LENGTH: 447 REFERENCE: NZ_JRYM01000065 LENGTH: 2704 REFERENCE: NZ_JRYM01000066 LENGTH: 1330 REFERENCE: NZ_JRYM01000067 LENGTH: 1829 REFERENCE: NZ_JRYM01000068 LENGTH: 3267 REFERENCE: NZ_JRYM01000069 LENGTH: 706 REFERENCE: NZ_JRYM01000070 LENGTH: 734 REFERENCE: NZ_JRYM01000071 LENGTH: 1501 REFERENCE: NZ_JRYM01000072 LENGTH: 1343 REFERENCE: NZ_JRYM01000073 LENGTH: 766 REFERENCE: NZ_JRYM01000074 LENGTH: 1893 REFERENCE: NZ_JRYM01000075 LENGTH: 8912 REFERENCE: NZ_JRYM01000076 LENGTH: 445 REFERENCE: NZ_JRYM01000077 LENGTH: 2751 REFERENCE: NZ_JRYM01000078 LENGTH: 2073 REFERENCE: NZ_JRYM01000079 LENGTH: 550 REFERENCE: NZ_JRYM01000080 LENGTH: 875 REFERENCE: NZ_JRYM01000081 LENGTH: 1022 REFERENCE: NZ_JRYM01000082 LENGTH: 489 REFERENCE: NZ_JRYM01000083 LENGTH: 541 REFERENCE: NZ_JRYM01000084 LENGTH: 823 REFERENCE: NZ_JRYM01000085 LENGTH: 1475 REFERENCE: NZ_JRYM01000086 LENGTH: 1481 REFERENCE: NZ_JRYM01000087 LENGTH: 2970 REFERENCE: NZ_JRYM01000088 LENGTH: 671 REFERENCE: NZ_JRYM01000089 LENGTH: 848 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/0.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/0.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/0.coverage.pdf deletion_propagation_pr_cutoff=9.70555e-05 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/1.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/1.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/1.coverage.pdf deletion_propagation_pr_cutoff=0.000284638 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/2.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/2.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/2.coverage.pdf deletion_propagation_pr_cutoff=0.000273539 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/3.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/3.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/3.coverage.pdf deletion_propagation_pr_cutoff=0.000202128 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/4.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/4.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/4.coverage.pdf deletion_propagation_pr_cutoff=0.000209519 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/5.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/5.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/5.coverage.pdf deletion_propagation_pr_cutoff=0.000147702 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/6.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/6.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/6.coverage.pdf deletion_propagation_pr_cutoff=0.000198385 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/7.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/7.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/7.coverage.pdf deletion_propagation_pr_cutoff=0.000897303 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/8.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/8.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/8.coverage.pdf deletion_propagation_pr_cutoff=0.000229658 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/9.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/9.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/9.coverage.pdf deletion_propagation_pr_cutoff=0.000156302 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/10.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/10.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/10.coverage.pdf deletion_propagation_pr_cutoff=0.000106254 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/11.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/11.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/11.coverage.pdf deletion_propagation_pr_cutoff=0.000118456 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/12.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/12.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/12.coverage.pdf deletion_propagation_pr_cutoff=0.000207876 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/13.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/13.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/13.coverage.pdf deletion_propagation_pr_cutoff=0.000198271 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/14.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/14.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/14.coverage.pdf deletion_propagation_pr_cutoff=0.000247561 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/15.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/15.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/15.coverage.pdf deletion_propagation_pr_cutoff=0.000151084 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/16.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/16.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/16.coverage.pdf deletion_propagation_pr_cutoff=0.000141007 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/17.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/17.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/17.coverage.pdf deletion_propagation_pr_cutoff=9.83579e-05 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/18.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/18.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/18.coverage.pdf deletion_propagation_pr_cutoff=0.000162247 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/19.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/19.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/19.coverage.pdf deletion_propagation_pr_cutoff=0.000254853 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/20.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/20.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/20.coverage.pdf deletion_propagation_pr_cutoff=0.000480237 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/21.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/21.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/21.coverage.pdf deletion_propagation_pr_cutoff=0.000178414 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/22.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/22.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/22.coverage.pdf deletion_propagation_pr_cutoff=0.000281647 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/23.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/23.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/23.coverage.pdf deletion_propagation_pr_cutoff=0.000896582 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/24.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/24.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/24.coverage.pdf deletion_propagation_pr_cutoff=0.000137133 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/25.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/25.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/25.coverage.pdf deletion_propagation_pr_cutoff=0.000105623 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/26.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/26.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/26.coverage.pdf deletion_propagation_pr_cutoff=0.000291685 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/27.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/27.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/27.coverage.pdf deletion_propagation_pr_cutoff=0.000149116 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/28.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/28.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/28.coverage.pdf deletion_propagation_pr_cutoff=0.000290085 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/29.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/29.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/29.coverage.pdf deletion_propagation_pr_cutoff=0.000292368 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/30.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/30.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/30.coverage.pdf deletion_propagation_pr_cutoff=0.000265942 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/31.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/31.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/31.coverage.pdf deletion_propagation_pr_cutoff=0.000168297 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/32.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/32.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/32.coverage.pdf deletion_propagation_pr_cutoff=0.000137355 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/33.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/33.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/33.coverage.pdf deletion_propagation_pr_cutoff=0.000435029 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/34.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/34.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/34.coverage.pdf deletion_propagation_pr_cutoff=0.00021321 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/35.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/35.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/35.coverage.pdf deletion_propagation_pr_cutoff=0.000133637 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/36.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/36.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/36.coverage.pdf deletion_propagation_pr_cutoff=0.000272748 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/37.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/37.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/37.coverage.pdf deletion_propagation_pr_cutoff=0.00012679 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/38.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/38.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/38.coverage.pdf deletion_propagation_pr_cutoff=0.000203488 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/39.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/39.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/39.coverage.pdf deletion_propagation_pr_cutoff=0.000396975 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/40.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/40.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/40.coverage.pdf deletion_propagation_pr_cutoff=0.000245405 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/41.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/41.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/41.coverage.pdf deletion_propagation_pr_cutoff=0.000213187 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/42.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/42.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/42.coverage.pdf deletion_propagation_pr_cutoff=0.00121843 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/43.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/43.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/43.coverage.pdf deletion_propagation_pr_cutoff=0.000916544 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/44.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/44.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/44.coverage.pdf deletion_propagation_pr_cutoff=0.000734738 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/45.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/45.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/45.coverage.pdf deletion_propagation_pr_cutoff=0.000559367 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/46.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/46.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/46.coverage.pdf deletion_propagation_pr_cutoff=0.00149204 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/47.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/47.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/47.coverage.pdf deletion_propagation_pr_cutoff=0.000540454 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/48.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/48.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/48.coverage.pdf deletion_propagation_pr_cutoff=0.000560525 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/49.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/49.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/49.coverage.pdf deletion_propagation_pr_cutoff=0.00102297 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/50.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/50.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/50.coverage.pdf deletion_propagation_pr_cutoff=0.000276403 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/51.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/51.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/51.coverage.pdf deletion_propagation_pr_cutoff=0.000252703 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/52.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/52.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/52.coverage.pdf deletion_propagation_pr_cutoff=0.000171001 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/53.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/53.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/53.coverage.pdf deletion_propagation_pr_cutoff=8.40621e-05 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/54.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/54.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/54.coverage.pdf deletion_propagation_pr_cutoff=0.000522451 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/55.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/55.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/55.coverage.pdf deletion_propagation_pr_cutoff=0.000283743 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/56.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/56.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/56.coverage.pdf deletion_propagation_pr_cutoff=0.00140971 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/57.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/57.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/57.coverage.pdf deletion_propagation_pr_cutoff=0.00182089 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/58.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/58.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/58.coverage.pdf deletion_propagation_pr_cutoff=0.00137568 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/59.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/59.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/59.coverage.pdf deletion_propagation_pr_cutoff=0.00236492 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/60.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/60.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/60.coverage.pdf deletion_propagation_pr_cutoff=0.000961538 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/61.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/61.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/61.coverage.pdf deletion_propagation_pr_cutoff=0.00137102 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/62.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/62.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/62.coverage.pdf deletion_propagation_pr_cutoff=0.00116913 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/63.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/63.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/63.coverage.pdf deletion_propagation_pr_cutoff=0.000874773 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/64.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/64.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/64.coverage.pdf deletion_propagation_pr_cutoff=0.000192786 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/65.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/65.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/65.coverage.pdf deletion_propagation_pr_cutoff=0.00188177 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/66.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/66.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/66.coverage.pdf deletion_propagation_pr_cutoff=0.00184553 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/67.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/67.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/67.coverage.pdf deletion_propagation_pr_cutoff=0.00129056 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/68.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/68.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/68.coverage.pdf deletion_propagation_pr_cutoff=0.00136437 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/69.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/69.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/69.coverage.pdf deletion_propagation_pr_cutoff=0.00180657 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/70.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/70.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/70.coverage.pdf deletion_propagation_pr_cutoff=0.0011492 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/71.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/71.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/71.coverage.pdf deletion_propagation_pr_cutoff=0.000529642 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/72.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/72.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/72.coverage.pdf deletion_propagation_pr_cutoff=0.00237023 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/73.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/73.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/73.coverage.pdf deletion_propagation_pr_cutoff=0.000953289 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/74.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/74.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/74.coverage.pdf deletion_propagation_pr_cutoff=0.00109817 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/75.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/75.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/75.coverage.pdf deletion_propagation_pr_cutoff=0.00163517 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/76.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/76.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/76.coverage.pdf deletion_propagation_pr_cutoff=0.00213201 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/77.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/77.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/77.coverage.pdf deletion_propagation_pr_cutoff=0.00169031 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/78.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/78.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/78.coverage.pdf deletion_propagation_pr_cutoff=0.00156403 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/79.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/79.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/79.coverage.pdf deletion_propagation_pr_cutoff=0.00226108 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/80.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/80.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/80.coverage.pdf deletion_propagation_pr_cutoff=0.00214967 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/81.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/81.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/81.coverage.pdf deletion_propagation_pr_cutoff=0.00174289 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/82.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/82.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/82.coverage.pdf deletion_propagation_pr_cutoff=0.00130189 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/83.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/83.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/83.coverage.pdf deletion_propagation_pr_cutoff=0.00129925 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/84.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/84.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/84.coverage.pdf deletion_propagation_pr_cutoff=0.00091747 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/85.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/85.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/85.coverage.pdf deletion_propagation_pr_cutoff=0.00193023 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/86.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/86.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/86.coverage.pdf deletion_propagation_pr_cutoff=0.000118992 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/87.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/87.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/87.coverage.pdf deletion_propagation_pr_cutoff=0.00171701 [system] R --vanilla < /home/groups/hpcbio/apps/breseq/breseq-0.32.0-Linux-x86_64/share/breseq/coverage_distribution.r > G1841MIC/03_candidate_junctions/88.unique_only_coverage_distribution.tab.r.log distribution_file=G1841MIC/03_candidate_junctions/88.unique_only_coverage_distribution.tab plot_file=G1841MIC/03_candidate_junctions/88.coverage.pdf deletion_propagation_pr_cutoff=0.000129865 [system] rm -f G1841MIC/03_candidate_junctions/best.unsorted.bam [system] rm -f G1841MIC/03_candidate_junctions/best.sam [system] rm -f G1841MIC/03_candidate_junctions/best.bam [system] rm -f G1841MIC/03_candidate_junctions/best.bam.bai [system] rm -f G1841MIC/03_candidate_junctions/0.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/0.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/0.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/1.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/1.unique_only_coverage_distribution.tab 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G1841MIC/03_candidate_junctions/81.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/82.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/82.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/82.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/83.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/83.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/83.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/84.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/84.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/84.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/85.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/85.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/85.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/86.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/86.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/86.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/87.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/87.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/87.unique_only_coverage_distribution.tab.r.log [system] rm -f G1841MIC/03_candidate_junctions/88.coverage.pdf [system] rm -f G1841MIC/03_candidate_junctions/88.unique_only_coverage_distribution.tab [system] rm -f G1841MIC/03_candidate_junctions/88.unique_only_coverage_distribution.tab.r.log +++ NOW PROCESSING Identifying junction candidates READ FILE::G1841MIC_R1.trimAQ ALIGNED READ:10000 CANDIDATE JUNCTIONS:1729 ALIGNED READ:20000 CANDIDATE JUNCTIONS:3258 READ FILE::G1841MIC_R2.trimAQ ALIGNED READ:30000 CANDIDATE JUNCTIONS:4636 ALIGNED READ:40000 CANDIDATE JUNCTIONS:5969 Passed alignment pairs examined: 51407 Taking top candidate junctions... Minimum number to keep: 100 Maximum number to keep: 5000 Maximum length to keep: 450319 bases Initial: Number = 675, Cumulative Length = 340632 bases Testing Pos Hash Score = 275, Num = 1, Length = 522 Testing Pos Hash Score = 265, Num = 1, Length = 522 Testing Pos Hash Score = 226, Num = 1, Length = 522 Testing Pos Hash Score = 217, Num = 1, Length = 522 Testing Pos Hash Score = 213, Num = 2, Length = 1042 Testing Pos Hash Score = 210, Num = 1, Length = 522 Testing Pos Hash Score = 209, Num = 1, Length = 501 Testing Pos Hash Score = 207, Num = 1, Length = 522 Testing Pos Hash Score = 205, Num = 2, Length = 1044 Testing Pos Hash Score = 204, Num = 1, Length = 522 Testing Pos Hash Score = 202, Num = 1, Length = 522 Testing Pos Hash Score = 180, Num = 1, Length = 522 Testing Pos Hash Score = 178, Num = 1, Length = 522 Testing Pos Hash Score = 175, Num = 1, Length = 522 Testing Pos Hash Score = 173, Num = 2, Length = 1044 Testing Pos Hash Score = 164, Num = 1, Length = 505 Testing Pos Hash Score = 159, Num = 1, Length = 474 Testing Pos Hash Score = 157, Num = 1, Length = 521 Testing Pos Hash Score = 156, Num = 1, Length = 505 Testing Pos Hash Score = 154, Num = 4, Length = 2041 Testing Pos Hash Score = 153, Num = 2, Length = 1012 Testing Pos Hash Score = 152, Num = 1, Length = 508 Testing Pos Hash Score = 151, Num = 2, Length = 974 Testing Pos Hash Score = 150, Num = 2, Length = 1039 Testing Pos Hash Score = 148, Num = 1, Length = 521 Testing Pos Hash Score = 147, Num = 2, Length = 1042 Testing Pos Hash Score = 146, Num = 5, Length = 2500 Testing Pos Hash Score = 145, Num = 3, Length = 1500 Testing Pos Hash Score = 144, Num = 4, Length = 2084 Testing Pos Hash Score = 143, Num = 3, Length = 1522 Testing Pos Hash Score = 142, Num = 2, Length = 1042 Testing Pos Hash Score = 141, Num = 1, Length = 502 Testing Pos Hash Score = 140, Num = 2, Length = 1029 Testing Pos Hash Score = 139, Num = 1, Length = 521 Testing Pos Hash Score = 138, Num = 2, Length = 1041 Testing Pos Hash Score = 137, Num = 5, Length = 2564 Testing Pos Hash Score = 136, Num = 1, Length = 500 Testing Pos Hash Score = 135, Num = 1, Length = 503 Testing Pos Hash Score = 134, Num = 1, Length = 520 Testing Pos Hash Score = 133, Num = 1, Length = 499 Testing Pos Hash Score = 132, Num = 4, Length = 2031 Testing Pos Hash Score = 131, Num = 1, Length = 500 Testing Pos Hash Score = 130, Num = 4, Length = 2081 Testing Pos Hash Score = 129, Num = 1, Length = 521 Testing Pos Hash Score = 128, Num = 4, Length = 2061 Testing Pos Hash Score = 127, Num = 2, Length = 1054 Testing Pos Hash Score = 126, Num = 4, Length = 2065 Testing Pos Hash Score = 125, Num = 1, Length = 550 Testing Pos Hash Score = 124, Num = 1, Length = 550 Testing Pos Hash Score = 123, Num = 4, Length = 2031 [Omitted Similar = 1] Testing Pos Hash Score = 122, Num = 3, Length = 1511 Testing Pos Hash Score = 121, Num = 2, Length = 1078 Testing Pos Hash Score = 119, Num = 0, Length = 0 [Omitted Similar = 1] Testing Pos Hash Score = 118, Num = 3, Length = 1511 Testing Pos Hash Score = 117, Num = 2, Length = 999 Testing Pos Hash Score = 116, Num = 1, Length = 504 Testing Pos Hash Score = 115, Num = 1, Length = 516 Testing Pos Hash Score = 114, Num = 1, Length = 500 Testing Pos Hash Score = 113, Num = 1, Length = 537 Testing Pos Hash Score = 112, Num = 1, Length = 500 Testing Pos Hash Score = 111, Num = 2, Length = 1011 Testing Pos Hash Score = 110, Num = 2, Length = 1001 Testing Pos Hash Score = 109, Num = 3, Length = 1444 Testing Pos Hash Score = 107, Num = 2, Length = 1039 Testing Pos Hash Score = 105, Num = 1, Length = 537 Testing Pos Hash Score = 104, Num = 2, Length = 1057 Testing Pos Hash Score = 102, Num = 3, Length = 1526 Testing Pos Hash Score = 101, Num = 2, Length = 1040 Testing Pos Hash Score = 100, Num = 2, Length = 1038 Testing Pos Hash Score = 99, Num = 4, Length = 2038 Testing Pos Hash Score = 98, Num = 2, Length = 1015 Testing Pos Hash Score = 94, Num = 0, Length = 0 [Omitted Similar = 1] Testing Pos Hash Score = 92, Num = 2, Length = 1045 Testing Pos Hash Score = 90, Num = 2, Length = 945 Testing Pos Hash Score = 89, Num = 1, Length = 522 Testing Pos Hash Score = 87, Num = 2, Length = 1028 Testing Pos Hash Score = 84, Num = 5, Length = 2504 Testing Pos Hash Score = 83, Num = 1, Length = 522 Testing Pos Hash Score = 81, Num = 1, Length = 515 Testing Pos Hash Score = 80, Num = 2, Length = 1066 Testing Pos Hash Score = 79, Num = 2, Length = 936 Testing Pos Hash Score = 77, Num = 2, Length = 1016 Testing Pos Hash Score = 76, Num = 2, Length = 1016 Testing Pos Hash Score = 75, Num = 1, Length = 550 Testing Pos Hash Score = 74, Num = 2, Length = 1070 Testing Pos Hash Score = 62, Num = 1, Length = 386 Testing Pos Hash Score = 61, Num = 1, Length = 503 Testing Pos Hash Score = 60, Num = 0, Length = 0 [Omitted Similar = 1] Testing Pos Hash Score = 59, Num = 0, Length = 0 [Omitted Similar = 1] Testing Pos Hash Score = 58, Num = 2, Length = 1023 Testing Pos Hash Score = 56, Num = 1, Length = 516 Testing Pos Hash Score = 53, Num = 1, Length = 525 [Omitted Similar = 1] Testing Pos Hash Score = 52, Num = 3, Length = 1585 Testing Pos Hash Score = 51, Num = 1, Length = 409 [Omitted Similar = 3] Testing Pos Hash Score = 50, Num = 2, Length = 1097 [Omitted Similar = 1] Testing Pos Hash Score = 49, Num = 2, Length = 912 Testing Pos Hash Score = 48, Num = 1, Length = 515 Testing Pos Hash Score = 46, Num = 1, Length = 558 [Omitted Similar = 1] Testing Pos Hash Score = 45, Num = 3, Length = 1552 Testing Pos Hash Score = 44, Num = 1, Length = 565 Testing Pos Hash Score = 40, Num = 1, Length = 386 Testing Pos Hash Score = 39, Num = 2, Length = 1026 Testing Pos Hash Score = 36, Num = 3, Length = 1524 Testing Pos Hash Score = 34, Num = 2, Length = 991 Testing Pos Hash Score = 33, Num = 0, Length = 0 [Omitted Similar = 1] Testing Pos Hash Score = 32, Num = 1, Length = 326 Testing Pos Hash Score = 30, Num = 0, Length = 0 [Omitted Similar = 1] Testing Pos Hash Score = 28, Num = 2, Length = 937 Testing Pos Hash Score = 27, Num = 2, Length = 900 Testing Pos Hash Score = 25, Num = 1, Length = 522 Testing Pos Hash Score = 23, Num = 5, Length = 2027 Testing Pos Hash Score = 21, Num = 1, Length = 500 Testing Pos Hash Score = 20, Num = 1, Length = 547 Testing Pos Hash Score = 19, Num = 2, Length = 851 Testing Pos Hash Score = 18, Num = 1, Length = 544 Testing Pos Hash Score = 17, Num = 1, Length = 503 Testing Pos Hash Score = 16, Num = 3, Length = 1323 Testing Pos Hash Score = 15, Num = 3, Length = 1688 Testing Pos Hash Score = 14, Num = 5, Length = 2879 Testing Pos Hash Score = 13, Num = 3, Length = 1696 Testing Pos Hash Score = 12, Num = 6, Length = 3204 Testing Pos Hash Score = 11, Num = 5, Length = 2662 Testing Pos Hash Score = 10, Num = 5, Length = 2788 Testing Pos Hash Score = 9, Num = 10, Length = 5287 Testing Pos Hash Score = 8, Num = 4, Length = 2109 [Omitted Similar = 1] Testing Pos Hash Score = 7, Num = 9, Length = 4243 Testing Pos Hash Score = 6, Num = 7, Length = 3461 Testing Pos Hash Score = 5, Num = 3, Length = 1519 Testing Pos Hash Score = 4, Num = 9, Length = 4290 [Omitted Similar = 2] Testing Pos Hash Score = 3, Num = 6, Length = 3101 [Omitted Similar = 2] Testing Pos Hash Score = 2, Num = 373, Length = 186904 [Omitted Similar = 2] Accepted: Number = 655, Pos Hash Score >= 2, Cumulative Length = 330307 bases [samtools] faidx G1841MIC/03_candidate_junctions/candidate_junction.fasta [system] rm -f G1841MIC/03_candidate_junctions/G1841MIC_R1.trimAQ.split.sam [system] rm -f G1841MIC/03_candidate_junctions/G1841MIC_R2.trimAQ.split.sam +++ NOW PROCESSING Re-alignment to junction candidates [system] bowtie2-build -q G1841MIC/03_candidate_junctions/candidate_junction.fasta G1841MIC/04_candidate_junction_alignment/candidate_junction [system] bowtie2 -t -p 8 --local -L 31 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,1,0.70 -k 2000 --reorder -x G1841MIC/04_candidate_junction_alignment/candidate_junction -U G1841MIC/01_sequence_conversion/G1841MIC_R1.trimAQ.converted.fastq -S G1841MIC/04_candidate_junction_alignment/G1841MIC_R1.trimAQ.candidate_junction.sam Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:57 3754607 reads; of these: 3754607 (100.00%) were unpaired; of these: 3589110 (95.59%) aligned 0 times 112843 (3.01%) aligned exactly 1 time 52654 (1.40%) aligned >1 times 4.41% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 [system] bowtie2 -t -p 8 --local -L 31 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,1,0.70 -k 2000 --reorder -x G1841MIC/04_candidate_junction_alignment/candidate_junction -U G1841MIC/01_sequence_conversion/G1841MIC_R2.trimAQ.converted.fastq -S G1841MIC/04_candidate_junction_alignment/G1841MIC_R2.trimAQ.candidate_junction.sam Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:54 3754606 reads; of these: 3754606 (100.00%) were unpaired; of these: 3586362 (95.52%) aligned 0 times 114893 (3.06%) aligned exactly 1 time 53351 (1.42%) aligned >1 times 4.48% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 [system] rm -f G1841MIC/04_candidate_junction_alignment/candidate_junction* +++ NOW PROCESSING Resolving best read alignments READ FILE:G1841MIC_R1.trimAQ READS:10000 READS:20000 READS:30000 READS:40000 READS:50000 READS:60000 READS:70000 READS:80000 READS:90000 READS:100000 READS:110000 READS:120000 READS:130000 READS:140000 READS:150000 READS:160000 READS:170000 READS:180000 READS:190000 READS:200000 READS:210000 READS:220000 READS:230000 READS:240000 READS:250000 READS:260000 READS:270000 READS:280000 READS:290000 READS:300000 READS:310000 READS:320000 READS:330000 READS:340000 READS:350000 READS:360000 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READS:7500000 >>> Error(s) in GenomeDiff format. FILE: <<< >>ERROR: Attempt to add duplicate of this existing entry from line NA: JC134.NZ_JRYM01000001221437-1NZ_JRYM0100005080-10alignment_overlap=56coverage_minus=68coverage_plus=36flanking_left=250flanking_right=80key=NZ_JRYM01000001__221437__-1__NZ_JRYM01000050__136__-1__56____250__80__0__0max_left=188max_left_minus=188max_left_plus=188max_min_left=78max_min_left_minus=78max_min_left_plus=0max_min_right=80max_min_right_minus=80max_min_right_plus=80max_pos_hash_score=340max_right=80max_right_minus=80max_right_plus=80neg_log10_pos_hash_p_value=NTpos_hash_score=74side_1_continuation=0side_1_overlap=56side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=104 Add a 'unique' tag to one if this is intentional. >>LINE: 0 JC164.NZ_JRYM01000001221437-1NZ_JRYM0100005080-10alignment_overlap=56coverage_minus=0coverage_plus=0flanking_left=250flanking_right=250key=NZ_JRYM01000001__221437__-1__NZ_JRYM01000050__136__-1__56____250__250__0__0__UDmax_left=0max_left_minus=0max_left_plus=0max_min_left=0max_min_left_minus=0max_min_left_plus=0max_min_right=0max_min_right_minus=0max_min_right_plus=0max_pos_hash_score=340max_right=0max_right_minus=0max_right_plus=0neg_log10_pos_hash_p_value=NTpos_hash_score=0reject=COVERAGE_EVENNESS_SKEWside_1_continuation=0side_1_overlap=56side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=0user_defined=1 >>ERROR: Attempt to add duplicate of this existing entry from line NA: JC118.NZ_JRYM01000011105-1NZ_JRYM010000521123-1-54alignment_overlap=-54coverage_minus=10coverage_plus=9flanking_left=250flanking_right=250key=NZ_JRYM01000011__105__-1__NZ_JRYM01000052__1123__-1__-54__GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATA__250__250__0__0__UDmax_left=189max_left_minus=189max_left_plus=189max_min_left=0max_min_left_minus=0max_min_left_plus=0max_min_right=20max_min_right_minus=20max_min_right_plus=20max_pos_hash_score=344max_right=20max_right_minus=20max_right_plus=20neg_log10_pos_hash_p_value=NTpos_hash_score=13side_1_continuation=0side_1_overlap=0side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=19unique_read_sequence=GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAuser_defined=1 Add a 'unique' tag to one if this is intentional. >>LINE: 0 JC131.NZ_JRYM01000011105-1NZ_JRYM010000521123-1-54alignment_overlap=-54coverage_minus=1coverage_plus=10flanking_left=105flanking_right=250key=NZ_JRYM01000011__105__-1__NZ_JRYM01000052__1123__-1__-54__GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATA__105__250__0__0max_left=84max_left_minus=71max_left_plus=84max_min_left=84max_min_left_minus=71max_min_left_plus=84max_min_right=83max_min_right_minus=0max_min_right_plus=83max_pos_hash_score=344max_right=90max_right_minus=84max_right_plus=90neg_log10_pos_hash_p_value=NTpos_hash_score=11side_1_continuation=0side_1_overlap=0side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=11unique_read_sequence=GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATA >>ERROR: Attempt to add duplicate of this existing entry from line NA: JC117.NZ_JRYM01000022406381NZ_JRYM0100003735329-10alignment_overlap=19coverage_minus=77coverage_plus=129flanking_left=136flanking_right=250key=NZ_JRYM01000022__40638__1__NZ_JRYM01000037__35348__-1__19____136__250__0__0max_left=115max_left_minus=115max_left_plus=115max_min_left=115max_min_left_minus=114max_min_left_plus=115max_min_right=114max_min_right_minus=114max_min_right_plus=113max_pos_hash_score=414max_right=225max_right_minus=222max_right_plus=225neg_log10_pos_hash_p_value=NTpos_hash_score=137side_1_continuation=0side_1_overlap=19side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=206 Add a 'unique' tag to one if this is intentional. >>LINE: 0 JC162.NZ_JRYM01000022406381NZ_JRYM0100003735329-10alignment_overlap=19coverage_minus=0coverage_plus=0flanking_left=250flanking_right=250key=NZ_JRYM01000022__40638__1__NZ_JRYM01000037__35348__-1__19____250__250__0__0__UDmax_left=0max_left_minus=0max_left_plus=0max_min_left=0max_min_left_minus=0max_min_left_plus=0max_min_right=0max_min_right_minus=0max_min_right_plus=0max_pos_hash_score=414max_right=0max_right_minus=0max_right_plus=0neg_log10_pos_hash_p_value=NTpos_hash_score=0reject=COVERAGE_EVENNESS_SKEWside_1_continuation=0side_1_overlap=19side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=0user_defined=1 >>ERROR: Attempt to add duplicate of this existing entry from line NA: JC121.NZ_JRYM01000037249-1NZ_JRYM01000087279610alignment_overlap=0coverage_minus=107coverage_plus=84flanking_left=249flanking_right=175key=NZ_JRYM01000037__249__-1__NZ_JRYM01000087__2796__1__0____249__175__1__0max_left=221max_left_minus=220max_left_plus=221max_min_left=124max_min_left_minus=119max_min_left_plus=124max_min_right=125max_min_right_minus=125max_min_right_plus=122max_pos_hash_score=452max_right=158max_right_minus=158max_right_plus=158neg_log10_pos_hash_p_value=NTpos_hash_score=134side_1_continuation=0side_1_overlap=0side_1_redundant=1side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=191 Add a 'unique' tag to one if this is intentional. >>LINE: 0 JC161.NZ_JRYM01000037249-1NZ_JRYM01000087279610alignment_overlap=0coverage_minus=0coverage_plus=0flanking_left=250flanking_right=250key=NZ_JRYM01000037__249__-1__NZ_JRYM01000087__2796__1__0____250__250__1__0__UDmax_left=0max_left_minus=0max_left_plus=0max_min_left=0max_min_left_minus=0max_min_left_plus=0max_min_right=0max_min_right_minus=0max_min_right_plus=0max_pos_hash_score=450max_right=0max_right_minus=0max_right_plus=0neg_log10_pos_hash_p_value=NTpos_hash_score=0reject=COVERAGE_EVENNESS_SKEWside_1_continuation=0side_1_overlap=0side_1_redundant=1side_2_continuation=1side_2_overlap=0side_2_redundant=0total_non_overlap_reads=0user_defined=1 >>ERROR: Attempt to add duplicate of this existing entry from line NA: JC109.NZ_JRYM01000040547711NZ_JRYM0100006211-54alignment_overlap=-54coverage_minus=153coverage_plus=171flanking_left=225flanking_right=250key=NZ_JRYM01000040__54771__1__NZ_JRYM01000062__1__1__-54__ACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACT__225__250__0__0max_left=190max_left_minus=186max_left_plus=190max_min_left=96max_min_left_minus=96max_min_left_plus=90max_min_right=98max_min_right_minus=98max_min_right_plus=98max_pos_hash_score=344max_right=189max_right_minus=189max_right_plus=188neg_log10_pos_hash_p_value=NTpos_hash_score=209side_1_continuation=0side_1_overlap=0side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=324unique_read_sequence=ACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACT Add a 'unique' tag to one if this is intentional. >>LINE: 0 JC158.NZ_JRYM01000040547711NZ_JRYM0100006211-54alignment_overlap=-54coverage_minus=0coverage_plus=0flanking_left=250flanking_right=250key=NZ_JRYM01000040__54771__1__NZ_JRYM01000062__1__1__-54__ACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACT__250__250__0__0__UDmax_left=0max_left_minus=0max_left_plus=0max_min_left=0max_min_left_minus=0max_min_left_plus=0max_min_right=0max_min_right_minus=0max_min_right_plus=0max_pos_hash_score=344max_right=0max_right_minus=0max_right_plus=0neg_log10_pos_hash_p_value=NTpos_hash_score=0reject=COVERAGE_EVENNESS_SKEWside_1_continuation=0side_1_overlap=0side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=0unique_read_sequence=ACCCCAGAACTTACTTATGCTGATTCCGGTGCGAAAATTGTTAATAAAGGTACTuser_defined=1 >>ERROR: Attempt to add duplicate of this existing entry from line NA: JC105.NZ_JRYM01000040547721NZ_JRYM010000752110alignment_overlap=20coverage_minus=136coverage_plus=138flanking_left=204flanking_right=250key=NZ_JRYM01000040__54772__1__NZ_JRYM01000075__1__1__20____204__250__0__0max_left=198max_left_minus=198max_left_plus=196max_min_left=112max_min_left_minus=112max_min_left_plus=112max_min_right=115max_min_right_minus=114max_min_right_plus=115max_pos_hash_score=412max_right=224max_right_minus=223max_right_plus=224neg_log10_pos_hash_p_value=NTpos_hash_score=205side_1_continuation=0side_1_overlap=20side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=274 Add a 'unique' tag to one if this is intentional. >>LINE: 0 JC160.NZ_JRYM01000040547721NZ_JRYM010000752110alignment_overlap=20coverage_minus=0coverage_plus=0flanking_left=250flanking_right=250key=NZ_JRYM01000040__54772__1__NZ_JRYM01000075__1__1__20____250__250__0__0__UDmax_left=0max_left_minus=0max_left_plus=0max_min_left=0max_min_left_minus=0max_min_left_plus=0max_min_right=0max_min_right_minus=0max_min_right_plus=0max_pos_hash_score=412max_right=0max_right_minus=0max_right_plus=0neg_log10_pos_hash_p_value=NTpos_hash_score=0reject=COVERAGE_EVENNESS_SKEWside_1_continuation=0side_1_overlap=20side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=0user_defined=1 >>ERROR: Attempt to add duplicate of this existing entry from line NA: JC132.NZ_JRYM0100004879-1NZ_JRYM01000088231-72alignment_overlap=-72coverage_minus=52coverage_plus=83flanking_left=79flanking_right=250key=NZ_JRYM01000048__79__-1__NZ_JRYM01000088__23__1__-72__ATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAG__79__250__0__0max_left=79max_left_minus=78max_left_plus=79max_min_left=79max_min_left_minus=78max_min_left_plus=79max_min_right=79max_min_right_minus=61max_min_right_plus=79max_pos_hash_score=308max_right=170max_right_minus=167max_right_plus=170neg_log10_pos_hash_p_value=NTpos_hash_score=90side_1_continuation=0side_1_overlap=0side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=135unique_read_sequence=ATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAG Add a 'unique' tag to one if this is intentional. >>LINE: 0 JC166.NZ_JRYM0100004879-1NZ_JRYM01000088231-72alignment_overlap=-72coverage_minus=0coverage_plus=0flanking_left=250flanking_right=250key=NZ_JRYM01000048__79__-1__NZ_JRYM01000088__23__1__-72__ATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAG__250__250__0__0__UDmax_left=0max_left_minus=0max_left_plus=0max_min_left=0max_min_left_minus=0max_min_left_plus=0max_min_right=0max_min_right_minus=0max_min_right_plus=0max_pos_hash_score=308max_right=0max_right_minus=0max_right_plus=0neg_log10_pos_hash_p_value=NTpos_hash_score=0reject=COVERAGE_EVENNESS_SKEWside_1_continuation=0side_1_overlap=0side_1_redundant=0side_2_continuation=0side_2_overlap=0side_2_redundant=0total_non_overlap_reads=0unique_read_sequence=ATTTTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGuser_defined=1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR STACK TRACE