Analyzing File: .//ref.chain chrI total_size: 230218 total_gaps: 44 total_gapsize: 81 total_blocks: 230137 chrII total_size: 813184 total_gaps: 58 total_gapsize: 128 total_blocks: 813056 chrIII total_size: 316620 total_gaps: 5 total_gapsize: 8 total_blocks: 316612 chrIV total_size: 1531933 total_gaps: 28 total_gapsize: 50 total_blocks: 1531883 chrIX total_size: 439888 total_gaps: 7 total_gapsize: 12 total_blocks: 439876 chrM total_size: 85779 total_gaps: 0 total_gapsize: 0 total_blocks: 85779 chrV total_size: 576874 total_gaps: 6 total_gapsize: 12 total_blocks: 576862 chrVI total_size: 270161 total_gaps: 16 total_gapsize: 30 total_blocks: 270131 chrVII total_size: 1090940 total_gaps: 58 total_gapsize: 80 total_blocks: 1090860 chrVIII total_size: 562643 total_gaps: 21 total_gapsize: 16 total_blocks: 562627 chrX total_size: 745751 total_gaps: 38 total_gapsize: 74 total_blocks: 745677 chrXI total_size: 666816 total_gaps: 22 total_gapsize: 426 total_blocks: 666390 chrXII total_size: 1078177 total_gaps: 13 total_gapsize: 8 total_blocks: 1078169 chrXIII total_size: 924431 total_gaps: 6 total_gapsize: 55 total_blocks: 924376 chrXIV total_size: 784333 total_gaps: 10 total_gapsize: 11 total_blocks: 784322 chrXV total_size: 1091291 total_gaps: 31 total_gapsize: 71 total_blocks: 1091220 chrXVI total_size: 948066 total_gaps: 12 total_gapsize: 11 total_blocks: 948055 chr: chrI chr: chrII chr: chrIII chr: chrIV chr: chrIX chr: chrM chr: chrV chr: chrVI chr: chrVII chr: chrVIII chr: chrX chr: chrXI chr: chrXII chr: chrXIII chr: chrXIV chr: chrXV chr: chrXVI ============= BLOCKS: ============= qName: chrI Size: 230092 qName: chrII Size: 812997 qName: chrIII Size: 316606 qName: chrIV Size: 1531854 qName: chrIX Size: 439868 qName: chrM Size: 85778 qName: chrV Size: 576855 qName: chrVI Size: 270114 qName: chrVII Size: 1090801 qName: chrVIII Size: 562605 qName: chrX Size: 745638 qName: chrXI Size: 666367 qName: chrXII Size: 1078155 qName: chrXIII Size: 924369 qName: chrXIV Size: 784311 qName: chrXV Size: 1091188 qName: chrXVI Size: 948042 ============= GAPS: ============= chrI 81 chrII 128 chrIII 8 chrIV 50 chrIX 12 chrM 0 chrV 12 chrVI 30 chrVII 80 chrVIII 16 chrX 74 chrXI 426 chrXII 8 chrXIII 55 chrXIV 11 chrXV 71 chrXVI 11 num_gaps before gap_extend_merge: 263 num_gaps after gap_extend_merge: 198 chrI chrII chrIII chrIV chrIX chrM chrV chrVI chrVII chrVIII chrX chrXI chrXII chrXIII chrXIV chrXV chrXVI Traceback (most recent call last): File "/home/yaximik/Programs/AirLift/src//2-generate_gaps/gaps_to_fasta.py", line 50, in seq_name = line.split(">")[1] IndexError: list index out of range [bwa_aln] 17bp reads: max_diff = 1 [bwa_aln] 24bp reads: max_diff = 2 [bwa_aln] 50bp reads: max_diff = 3 [bwa_aln] 81bp reads: max_diff = 4 [bwa_aln] 114bp reads: max_diff = 5 [bwa_aln] 149bp reads: max_diff = 6 [bwa_aln] 184bp reads: max_diff = 7 [bwa_aln] 221bp reads: max_diff = 8 [bwa_aln_core] calculate SA coordinate... 1.61 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 3655 sequences have been processed. [main] Version: 0.7.17-r1188 [main] CMD: /home/yaximik/Programs/AirLift/dependencies/bin/bwa aln -n 0.08 -t 15 ../../sacCer2//ref.fa .//ref_kmer_gaps.fasta [main] Real time: 0.146 sec; CPU: 1.620 sec [bwa_aln_core] convert to sequence coordinate... 0.02 sec [bwa_aln_core] refine gapped alignments... 0.25 sec [bwa_aln_core] print alignments... 0.01 sec [bwa_aln_core] 3655 sequences have been processed. [main] Version: 0.7.17-r1188 [main] CMD: /home/yaximik/Programs/AirLift/dependencies/bin/bwa samse ../../sacCer2//ref.fa .//ref_aligned_gaps.sai .//ref_kmer_gaps.fasta [main] Real time: 0.298 sec; CPU: 0.294 sec Error: Cannot find sort-bed binary required for sorting BED output convert2bed version: 2.4.40 author: Alex Reynolds Usage: $ convert2bed --input=fmt [--output=fmt] [options] < input > output Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF and WIG genomic formats to BED or BEDOPS Starch (compressed BED) Input can be a regular file or standard input piped in using the hyphen character ('-'): $ some_upstream_process ... | convert2bed --input=fmt - > output Input (required): --input=[bam|gff|gtf|gvf|psl|rmsk|sam|vcf|wig] (-i ) Genomic format of input file (required) Output: --output=[bed|starch] (-o ) Format of output file, either BED or BEDOPS Starch (optional, default is BED) Other processing options: --do-not-sort (-d) Do not sort BED output with sort-bed (not compatible with --output=starch) --max-mem= (-m ) Sets aside memory for sorting BED output. For example, can be 8G, 8000M or 8000000000 to specify 8 GB of memory (default is 2G) --sort-tmpdir= (-r ) Optionally sets [dir] as temporary directory for sort data, when used in conjunction with --max-mem=[value], instead of the host's operating system default temporary directory --starch-bzip2 (-z) Used with --output=starch, the compressed output explicitly applies the bzip2 algorithm to compress intermediate data (default is bzip2) --starch-gzip (-g) Used with --output=starch, the compressed output applies gzip compression on intermediate data --starch-note="xyz..." (-e "xyz...") Used with --output=starch, this adds a note to the Starch archive metadata --help | --help[-bam|-gff|-gtf|-gvf|-psl|-rmsk|-sam|-vcf|-wig] (-h | -h ) Show general help message (or detailed help for a specified input format) --version (-w) Show application version Error: Unable to open file .//bedfiles/ref//*.bed. Exiting. mv: ‘.//bedfiles/ref//merged_*.bed’ and ‘.//bedfiles/ref//merged_*.bed’ are the same file Analyzing File: .//ref.chain qName: chrI Size: 230207 qName: chrII Size: 813177 qName: chrIII Size: 316616 qName: chrIV Size: 1531918 qName: chrIX Size: 439884 qName: chrM Size: 85778 qName: chrV Size: 576868 qName: chrVI Size: 270147 qName: chrVII Size: 1090946 qName: chrVIII Size: 562642 qName: chrX Size: 745741 qName: chrXI Size: 666453 qName: chrXII Size: 1078174 qName: chrXIII Size: 924428 qName: chrXIV Size: 784332 qName: chrXV Size: 1091288 qName: chrXVI Size: 948061 merged -- total size: 12156660 -- lines : 17 retired -- total size: 0 -- lines : 0 ref.chain usage: CrossMap.py [-h] [-v] {bed,bam,gff,wig,bigwig,vcf,gvcf,maf,region,viewchain} ... CrossMap.py: error: unrecognized arguments: - cat: .//bedfiles/ref/constant/crossmap_final.bed: No such file or directory java -ea -Xmx1g -cp /home/yaximik/Programs/AirLift/dependencies/bin/current/ jgi.RenameReads ow=t in=stdin.fastq out=.//bedfiles/ref/realigned_reads//singletons.fastq prefix=realigned_singleton java -ea -Xmx1g -cp /home/yaximik/Programs/AirLift/dependencies/bin/current/ jgi.RenameReads ow=t in=stdin.fastq out=.//bedfiles/ref/realigned_reads//fixed_reads_2.fastq prefix=realigned java -ea -Xmx1g -cp /home/yaximik/Programs/AirLift/dependencies/bin/current/ jgi.RenameReads ow=t in=stdin.fastq out=.//bedfiles/ref/realigned_reads//fixed_reads_1.fastq prefix=realigned java -ea -Xmx48811m -cp /home/yaximik/Programs/AirLift/dependencies/bin/current/ jgi.SplitPairsAndSingles rp overwrite=t in=.//bedfiles/ref/realigned_reads//reads_1.fastq in2=.//bedfiles/ref/realigned_reads//reads_2.fastq out=/dev/fd/63 out2=/dev/fd/62 outs=/dev/fd/61 ain=t Executing jgi.RenameReads [ow=t, in=stdin.fastq, out=.//bedfiles/ref/realigned_reads//fixed_reads_1.fastq, prefix=realigned] Executing jgi.RenameReads [ow=t, in=stdin.fastq, out=.//bedfiles/ref/realigned_reads//fixed_reads_2.fastq, prefix=realigned] Executing jgi.RenameReads [ow=t, in=stdin.fastq, out=.//bedfiles/ref/realigned_reads//singletons.fastq, prefix=realigned_singleton] Executing jgi.SplitPairsAndSingles [rp, overwrite=t, in=.//bedfiles/ref/realigned_reads//reads_1.fastq, in2=.//bedfiles/ref/realigned_reads//reads_2.fastq, out=/dev/fd/63, out2=/dev/fd/62, outs=/dev/fd/61, ain=t] Set INTERLEAVED to false Unspecified format for output /dev/fd/63; defaulting to fastq. Unspecified format for output /dev/fd/62; defaulting to fastq. Unspecified format for output /dev/fd/61; defaulting to fastq. Started output stream. Input: 0 reads 0 bases. Result: 0 reads (NaN%) 0 bases (NaN%) Pairs: 0 reads (NaN%) 0 bases (NaN%) Singletons: 0 reads (NaN%) 0 bases (NaN%) Time: 0.045 seconds. Reads Processed: 0 0.00k reads/sec Bases Processed: 0 0.00m bases/sec [M::bwa_idx_load_from_disk] read 0 ALT contigs Time: 0.177 seconds. [main] Version: 0.7.17-r1188 [main] CMD: /home/yaximik/Programs/AirLift/dependencies/bin/bwa mem -R @RG\tID:ERR1938683\tSM:ERR1938683\tPL:illumina\tLB:ERR1938683 -t 10 ../../sacCer3//ref.fa .//bedfiles/ref/realigned_reads/reads_1.fastq .//bedfiles/ref/realigned_reads/reads_2.fastq [main] Real time: 0.020 sec; CPU: 0.021 sec Time: 0.209 seconds. [M::bwa_idx_load_from_disk] read 0 ALT contigs [main] Version: 0.7.17-r1188 [main] CMD: /home/yaximik/Programs/AirLift/dependencies/bin/bwa mem -R @RG\tID:ERR1938683\tSM:ERR1938683\tPL:illumina\tLB:ERR1938683 -t 10 ../../sacCer3//ref.fa .//bedfiles/ref/realigned_reads/singletons.fastq [main] Real time: 0.016 sec; CPU: 0.018 sec merge: unrecognized option '--write-index' Usage: samtools merge [-nurlf] [-h inh.sam] [-b ] [ ... ] Options: -n Input files are sorted by read name -t TAG Input files are sorted by TAG value -r Attach RG tag (inferred from file names) -u Uncompressed BAM output -f Overwrite the output BAM if exist -1 Compress level 1 -l INT Compression level, from 0 to 9 [-1] -R STR Merge file in the specified region STR [all] -h FILE Copy the header in FILE to [in1.bam] -c Combine @RG headers with colliding IDs [alter IDs to be distinct] -p Combine @PG headers with colliding IDs [alter IDs to be distinct] -s VALUE Override random seed -b FILE List of input BAM filenames, one per line [null] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] Time: 0.253 seconds.