{"action":"created","issue":{"url":"https://api.github.com/repos/Oshlack/STRetch/issues/45","repository_url":"https://api.github.com/repos/Oshlack/STRetch","labels_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45/comments","events_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45/events","html_url":"https://github.com/Oshlack/STRetch/issues/45","id":387170177,"node_id":"MDU6SXNzdWUzODcxNzAxNzc=","number":45,"title":"error on bam files","user":{"login":"hrafehi","id":34467267,"node_id":"MDQ6VXNlcjM0NDY3MjY3","avatar_url":"https://avatars3.githubusercontent.com/u/34467267?v=4","gravatar_id":"","url":"https://api.github.com/users/hrafehi","html_url":"https://github.com/hrafehi","followers_url":"https://api.github.com/users/hrafehi/followers","following_url":"https://api.github.com/users/hrafehi/following{/other_user}","gists_url":"https://api.github.com/users/hrafehi/gists{/gist_id}","starred_url":"https://api.github.com/users/hrafehi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hrafehi/subscriptions","organizations_url":"https://api.github.com/users/hrafehi/orgs","repos_url":"https://api.github.com/users/hrafehi/repos","events_url":"https://api.github.com/users/hrafehi/events{/privacy}","received_events_url":"https://api.github.com/users/hrafehi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-12-04T08:26:22Z","updated_at":"2018-12-04T23:54:05Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI had the following error when trying to run sTRetch on bam files:\r\n\r\n[]\t======================================== Stage str_targets =========================================\r\nERROR: An output containing or ending with '.bed' was referenced.\r\n\r\nHowever such an output was not in the outputs specified by an enclosing transform / filter / produce statement.\r\n\r\nValid outputs according to the enclosing block are: 24644-1-fixed.slop.bam \r\n\r\nThanks\r\n\r\nHaloom"},"comment":{"url":"https://api.github.com/repos/Oshlack/STRetch/issues/comments/444304785","html_url":"https://github.com/Oshlack/STRetch/issues/45#issuecomment-444304785","issue_url":"https://api.github.com/repos/Oshlack/STRetch/issues/45","id":444304785,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NDMwNDc4NQ==","user":{"login":"hrafehi","id":34467267,"node_id":"MDQ6VXNlcjM0NDY3MjY3","avatar_url":"https://avatars3.githubusercontent.com/u/34467267?v=4","gravatar_id":"","url":"https://api.github.com/users/hrafehi","html_url":"https://github.com/hrafehi","followers_url":"https://api.github.com/users/hrafehi/followers","following_url":"https://api.github.com/users/hrafehi/following{/other_user}","gists_url":"https://api.github.com/users/hrafehi/gists{/gist_id}","starred_url":"https://api.github.com/users/hrafehi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hrafehi/subscriptions","organizations_url":"https://api.github.com/users/hrafehi/orgs","repos_url":"https://api.github.com/users/hrafehi/repos","events_url":"https://api.github.com/users/hrafehi/events{/privacy}","received_events_url":"https://api.github.com/users/hrafehi/received_events","type":"User","site_admin":false},"created_at":"2018-12-04T23:54:05Z","updated_at":"2018-12-04T23:54:05Z","author_association":"NONE","body":"\r\n####################################################################################################\r\n# Starting pipeline at Wed Dec 05 10:50:44 AEDT 2018\r\n# Input files:  [/stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam, /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam, /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam]\r\n# Output Log:  .bpipe/logs/6316.log\r\n# Stage set_sample_info (HD-1-fixed)\r\n# Stage set_sample_info (HD-12-fixed)\r\n# Stage set_sample_info (HD-10-fixed)\r\n# Stage mosdepth_dist (1)\r\n# Stage mosdepth_dist (1)\r\n# Stage mosdepth_dist (1)\r\n# Stage init_shard (1)\r\n# Stage init_shard (5)\r\n# Stage init_shard (10)\r\n# Stage init_shard (1)\r\n# Stage init_shard (8)\r\n# Stage align_bwa_bam (1)\r\n# Stage init_shard (7)\r\n# Stage init_shard (11)\r\n# Stage init_shard (1)\r\n# Stage init_shard (3)\r\n# Stage init_shard (8)\r\n# Stage init_shard (7)\r\n# Stage init_shard (9)\r\n# Stage init_shard (10)\r\n# Stage init_shard (2)\r\n# Stage align_bwa_bam (8)\r\n# Stage init_shard (12)\r\n# Stage init_shard (12)\r\n# Stage init_shard (2)\r\n# Stage init_shard (2)\r\n# Stage init_shard (7)\r\n# Stage init_shard (3)\r\n# Stage init_shard (6)\r\n# Stage init_shard (6)\r\n# Stage init_shard (8)\r\n# Stage init_shard (4)\r\n# Stage init_shard (11)\r\n# Stage init_shard (4)\r\n# Stage init_shard (9)\r\n# Stage init_shard (6)\r\n# Stage init_shard (11)\r\n# Stage align_bwa_bam (10)\r\n# Stage init_shard (3)\r\n# Stage align_bwa_bam (12)\r\n# Stage init_shard (4)\r\n# Stage align_bwa_bam (11)\r\n# Stage init_shard (5)\r\n# Stage align_bwa_bam (7)\r\n# Stage align_bwa_bam (5)\r\n# Stage init_shard (10)\r\n# Stage init_shard (12)\r\n# Stage align_bwa_bam (1)\r\n# Stage align_bwa_bam (3)\r\n# Stage init_shard (9)\r\n# Stage align_bwa_bam (10)\r\n# Stage align_bwa_bam (1)\r\n# Stage init_shard (5)\r\n# Stage align_bwa_bam (2)\r\n# Stage align_bwa_bam (9)\r\n# Stage align_bwa_bam (2)\r\n# Stage align_bwa_bam (12)\r\n# Stage align_bwa_bam (8)\r\n# Stage align_bwa_bam (7)\r\n# Stage align_bwa_bam (11)\r\n# Stage align_bwa_bam (8)\r\n# Stage align_bwa_bam (6)\r\n# Stage align_bwa_bam (4)\r\n# Stage align_bwa_bam (6)\r\n# Stage align_bwa_bam (3)\r\n# Stage align_bwa_bam (4)\r\n# Stage align_bwa_bam (11)\r\n# Stage align_bwa_bam (7)\r\n# Stage align_bwa_bam (5)\r\n# Stage align_bwa_bam (2)\r\n# Stage align_bwa_bam (6)\r\n# Stage align_bwa_bam (4)\r\n# Stage align_bwa_bam (5)\r\n# Stage align_bwa_bam (9)\r\n# Stage align_bwa_bam (3)\r\n# Stage align_bwa_bam (12)\r\n# Stage align_bwa_bam (10)\r\n# Stage align_bwa_bam (9)\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 6,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.6.STRdecoy.bam -T HD-1-fixed.6.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 4,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.4.STRdecoy.bam -T HD-1-fixed.4.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 8,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.8.STRdecoy.bam -T HD-10-fixed.8.STRdecoy\r\nsoftware/apps/STRetch-recent/STRetch/tools/bin/mosdepth -n -t 8 HD-10-fixed /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 8,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.8.STRdecoy.bam -T HD-1-fixed.8.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 10,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.10.STRdecoy.bam -T HD-1-fixed.10.STRdecoy\r\nsoftware/apps/STRetch-recent/STRetch/tools/bin/mosdepth -n -t 8 HD-1-fixed /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 1,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.1.STRdecoy.bam -T HD-10-fixed.1.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 12,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.12.STRdecoy.bam -T HD-1-fixed.12.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 11,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.11.STRdecoy.bam -T HD-12-fixed.11.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 1,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.1.STRdecoy.bam -T HD-12-fixed.1.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 12,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.12.STRdecoy.bam -T HD-12-fixed.12.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 2,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.2.STRdecoy.bam -T HD-1-fixed.2.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 2,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.2.STRdecoy.bam -T HD-12-fixed.2.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 5,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.5.STRdecoy.bam -T HD-12-fixed.5.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 7,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.7.STRdecoy.bam -T HD-12-fixed.7.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 1,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.1.STRdecoy.bam -T HD-1-fixed.1.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 3,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.3.STRdecoy.bam -T HD-10-fixed.3.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 5,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.5.STRdecoy.bam -T HD-1-fixed.5.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 6,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.6.STRdecoy.bam -T HD-10-fixed.6.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 11,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.11.STRdecoy.bam -T HD-10-fixed.11.STRdecoy\r\nsoftware/apps/STRetch-recent/STRetch/tools/bin/mosdepth -n -t 8 HD-12-fixed /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 2,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.2.STRdecoy.bam -T HD-10-fixed.2.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 7,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.7.STRdecoy.bam -T HD-1-fixed.7.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 11,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.11.STRdecoy.bam -T HD-1-fixed.11.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 6,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.6.STRdecoy.bam -T HD-12-fixed.6.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 10,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.10.STRdecoy.bam -T HD-10-fixed.10.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 5,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.5.STRdecoy.bam -T HD-10-fixed.5.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 12,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.12.STRdecoy.bam -T HD-10-fixed.12.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 4,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.4.STRdecoy.bam -T HD-10-fixed.4.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 3,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.3.STRdecoy.bam -T HD-12-fixed.3.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 9,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.9.STRdecoy.bam -T HD-10-fixed.9.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 3,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.3.STRdecoy.bam -T HD-1-fixed.3.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 9,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-1-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-1-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-1-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-1-fixed.9.STRdecoy.bam -T HD-1-fixed.9.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 10,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.10.STRdecoy.bam -T HD-12-fixed.10.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 4,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.4.STRdecoy.bam -T HD-12-fixed.4.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 8,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.8.STRdecoy.bam -T HD-12-fixed.8.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 7,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-10-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-10-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-10-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-10-fixed.7.STRdecoy.bam -T HD-10-fixed.7.STRdecoy\r\nset -o pipefail;  java -Xmx16g -Dsamjdk.reference_fasta=$CRAM_REF  -jar software/apps/bazam/bazam -pad 5 -n 6 -L software/apps/STRetch-recent/STRetch//reference-data/hg19.simpleRepeat_period1-6_dedup.sorted.bed -s 9,12 -bam /stornext/Bioinf/run_STRetch_milton_bam/bams/HD-12-fixed.bam | software/apps/STRetch-recent/STRetch/tools/bin/bwa mem -p -M -t 7                     -R \"@RG\\tID:HD-12-fixed\\tPL:illumina\\tPU:NA\\tLB:NA\\tSM:HD-12-fixed\"                     software/apps/STRetch-recent/STRetch/reference-data/hg19.STRdecoys.sorted.fasta - |                 software/apps/STRetch-recent/STRetch/tools/bin/samtools view -bSuh - | software/apps/STRetch-recent/STRetch/tools/bin/samtools sort -o HD-12-fixed.9.STRdecoy.bam -T HD-12-fixed.9.STRdecoy\r\n# ################ Finished at Wed Dec 05 10:50:48 AEDT 2018 Duration = 3.794 seconds ################\r\n\r\n"}}
{"actor":{"display_login":"hrafehi"}}