ryanlayer
commented
5 years ago I am guessing that there are no named read groups in the bam. Can you confirm?
On Nov 1, 2018, at 12:21 PM, Arda Soylev notifications@github.com wrote:
Hello, I'm running lumpyexpress with CHM13, which has 23 libraries. It seems to be running fine but no output is generated. It works fine with other bams.
lumpyexpress -B /mnt/storage1/projects/chm13/ilmn/CHM13.GRCh37.bam -o chm13_grc37_new_latest.vcf -v Sourcing executables from /mnt/compgen/inhouse/bin/lumpyexpress.config ...
Checking for required python modules (/usr/bin/python)...
create temporary directory
/usr/bin/python /mnt/compgen/inhouse/src/lumpy/lumpy-sv//scripts/bamkit/bamgroupreads.py --fix_flags -i /mnt/storage1/projects/chm13/ilmn/CHM13.GRCh37.bam -r HGT55.2,HGT55.3,HGT55.4,HGT55.5,HGT55.6,HGT55.7,HGT55.8,HHYFM.1,HHYFM.2,HHYFM.3,HHYFM.4,HHYFM.5,HHYFM.6,HHYFM.7,HJ2HJ.1,HJ2HJ.2,HJ2HJ.3,HJ2HJ.4,HJ2HJ.5,HJ2HJ.6,HJ2HJ.7,HJ2HJ.8,HKK7N.7 \ | /mnt/compgen/inhouse/bin/samblaster --acceptDupMarks --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 \ --splitterFile chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/spl_pipe --discordantFile chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/disc_pipe \ | /mnt/compgen/inhouse/bin/samtools view -S /dev/stdin \ | gawk '{ if (NR<=1000000) print > "/dev/stdout" ; else print > "/dev/null" }' \ | /usr/bin/python /mnt/compgen/inhouse/src/lumpy/lumpy-sv//scripts/pairend_distro.py -r 151 -X 4 -N 1000000 -o chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/chm13_grc37_new_latest.vcf.sample1.lib1.x4.histo \ > chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/chm13_grc37_new_latest.vcf.sample1.lib1.insert.stats /mnt/compgen/inhouse/bin/samtools view -S -u chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/spl_pipe \ | /mnt/compgen/inhouse/bin/samtools sort -m 1G -T chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/spl -o chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/chm13_grc37_new_latest.vcf.sample1.lib1.splitters.bam /dev/stdin /mnt/compgen/inhouse/bin/samtools view -S -u chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/disc_pipe \ | /mnt/compgen/inhouse/bin/samtools sort -m 1G -T chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/disc -o chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/chm13_grc37_new_latest.vcf.sample1.lib1.discordants.bam /dev/stdinsamblaster: Version 0.1.24 samblaster: Inputting from stdin samblaster: Outputting to stdout samblaster: Opening chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/disc_pipe for write. samblaster: Opening chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/spl_pipe for write. samblaster: Loaded 85 header sequence entries. Warning: 6078801 unmatched name groups samblaster: Output 5214709 discordant read pairs to chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/disc_pipe samblaster: Output 0 split reads to chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/spl_pipe samblaster: Marked 0 of 426801819 (0.00%) read ids as duplicates using 2728k memory in 54M23S(3262.620S) CPU seconds and 5H1M29S(18089S) wall time. [bam_sort_core] merging from 4 files and 1 in-memory blocks... Removed 881 outliers with isize >= 1301
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asylvz
Hello, I'm running lumpyexpress with CHM13, which has 23 libraries. It seems to be running fine but no output is generated. It works fine with other bams.
lumpyexpress -B /mnt/storage1/projects/chm13/ilmn/CHM13.GRCh37.bam -o chm13_grc37_new_latest.vcf -v Sourcing executables from /mnt/compgen/inhouse/bin/lumpyexpress.config ...
Checking for required python modules (/usr/bin/python)...
samblaster: Version 0.1.24 samblaster: Inputting from stdin samblaster: Outputting to stdout samblaster: Opening chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/disc_pipe for write. samblaster: Opening chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/spl_pipe for write. samblaster: Loaded 85 header sequence entries. Warning: 6078801 unmatched name groups samblaster: Output 5214709 discordant read pairs to chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/disc_pipe samblaster: Output 0 split reads to chm13_grc37_new_latest.vcf.1QkwI2BAqSiC/spl_pipe samblaster: Marked 0 of 426801819 (0.00%) read ids as duplicates using 2728k memory in 54M23S(3262.620S) CPU seconds and 5H1M29S(18089S) wall time. [bam_sort_core] merging from 4 files and 1 in-memory blocks... Removed 881 outliers with isize >= 1301