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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
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Error -running speedseq SV - missing pair end parameters:mean stdev #136

Open bioteksampath opened 5 years ago

bioteksampath commented 5 years ago

Hi, When i use the test data, speedseq ran well and produced expected SNV and SV outputs. however, when i ran with my 7 samples, SNV output was generated and I'm getting the following error for the SV call.

missing pair end parameters:mean stdev

Not sure how to proceed? I found that lu_sv.Bna_Mi1-7.sv.vcf.sample1.lib1.insert.stats contains mean:NA stdev:NA

My cmd was: /mnt/HNAS_NLSAS/home/AGR.GC.CA/perumals/SV/SVpipeline/speedseq/bin/speedseq sv \ -t $NSLOTS \ -R ~/SV/Bna_Mi1-7/ref/Bna_genome_v3.1.50k.fa \ -o lu_sv.Bna_Mi1-7 \ -B ~/SV/Bna_Mi1-7/bams/Bna_Mi1.sorted.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi2.sorted.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi3.sorted.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi4.sorted.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi5.sorted.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi6.sorted.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi7.sorted.bam \ -S ~/SV/Bna_Mi1-7/bams/Bna_Mi1.splitters.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi2.splitters.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi3.splitters.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi4.splitters.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi5.splitters.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi6.splitters.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi7.splitters.bam \ -D ~/SV/Bna_Mi1-7/bams/Bna_Mi1.discordent.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi2.discordent.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi3.discordent.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi4.discordent.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi5.discordent.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi6.discordent.bam, ~/SV/Bna_Mi1-7/bams/Bna_Mi7.discordent.bam

I try to change the parameter manually and run the below command bit no avail. mean:105,stdev:500

mnt/HNAS_NLSAS/home/AGR.GC.CA/sanjithmk/SVpipeline/speedseq//bin/lumpy \ -t lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf \ -msw 4 \ -tt 0 \ \ -pe bam_file:lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.discordants.bam,histo_file:lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.lib1.x4.histo,mean:105,stdev:500,read_length:100,min_non_overlap:100,discordant_z:5,back_distance:10,weight:1,id:HWI-ST538_240_D131HACXX3,min_mapping_threshold:20,read_group:HWI-ST538_240_D131HACXX_3 \ -sr bam_file:lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:HWI-ST538_240_D131HACXX3,min_clip:20,read_group:HWI-ST538_240_D131HACXX_3 \

lu_sv.Bna_Mi1-7.xT45QubyybIW/lu_sv.Bna_Mi1-7.sv.vcf

your help will be much appriciated ############Sterr out################### Checking for required python modules (/home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/python2.7)...

    create temporary directory

Running LUMPY express Sourcing executables from /mnt/HNAS_NLSAS/home/AGR.GC.CA/perumals/SV/SVpipeline/speedseq/bin/speedseq.config ...

Checking for required python modules (/home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/python2.7)...

create temporary directory

    /home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/python2.7 /mnt/HNAS_NLSAS/home/AGR.GC.CA/sanjithmk/SVpipeline/speedseq//bin/bamgroupreads.py --fix_flags -i /home/AAFC-AAC/perumals/SV/Bna_Mi1-7/bams/Bna_Mi1.sorted.bam -r HWI-ST538_240_D131HACXX_3 \
    | /mnt/HNAS_NLSAS/home/AGR.GC.CA/sanjithmk/SVpipeline/speedseq//bin/samblaster --acceptDupMarks --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 \
    --splitterFile lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/spl_pipe --discordantFile lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/disc_pipe \
    | /home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/samtools view -S /dev/stdin \
    | gawk '{ if (NR<=1000000) print > "/dev/stdout" ; else print > "/dev/null" }' \
    | /home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/python2.7 /mnt/HNAS_NLSAS/home/AGR.GC.CA/sanjithmk/SVpipeline/speedseq//bin/pairend_distro.py -r 100 -X 4 -N 1000000 -o lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.lib1.x4.histo \
    > lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.lib1.insert.stats

    /home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/samtools view -S -u lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/spl_pipe \
    | /home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/samtools sort -m 1G -T  lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/spl -o lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.lib1.splitters.bam /dev/stdin
    /home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/samtools view -S -u lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/disc_pipe \
    | /home/AAFC-AAC/sanjithmk/miniconda3/envs/svenv/bin/samtools sort -m 1G -T  lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/disc -o lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.lib1.discordants.bam /dev/stdin

samblaster: Version 0.1.22 samblaster: Inputting from stdin samblaster: Outputting to stdout samblaster: Opening lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/disc_pipe for write. samblaster: Opening lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/spl_pipe for write. samblaster: Loaded 80 header sequence entries. Warning: 1532622 unmatched name groups samblaster: Output 132996660 discordant read pairs to lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/disc_pipe samblaster: Output 0 split reads to lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/spl_pipe samblaster: Marked 0 of 139200626 (0.00%) read ids as duplicates using 1152k memory in 9M51S(590.694S) CPU seconds and 2H31M35S(9095S) wall time. Warning: only 34 elements in distribution (min: 1000) [bam_sort_core] merging from 85 files and 1 in-memory blocks... Running LUMPY...

/mnt/HNAS_NLSAS/home/AGR.GC.CA/sanjithmk/SVpipeline/speedseq//bin/lumpy \ -t lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf \ -msw 4 \ -tt 0 \ \ -pe bam_file:lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.discordants.bam,histo_file:lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.lib1.x4.histo,mean:NA,stdev:NA,read_length:100,min_non_overlap:100,discordant_z:5,back_distance:10,weight:1,id:HWI-ST538_240_D131HACXX3,min_mapping_threshold:20,read_group:HWI-ST538_240_D131HACXX_3 \ -sr bam_file:lu_sv.Bna_Mi1-7.xT45QubyybIW/temp_lumpyexpress/lu_sv.Bna_Mi1-7.sv.vcf.sample1.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:HWI-ST538_240_D131HACXX3,min_clip:20,read_group:HWI-ST538_240_D131HACXX_3 \

lu_sv.Bna_Mi1-7.xT45QubyybIW/lu_sv.Bna_Mi1-7.sv.vcf missing pair end parameters:mean stdev