Failed execution for demo data

[snewmanSema4]

Trying to run the demo example on my local computer. First attempt ran for two days then failed. Second example, I made a smaller region:
chr21 47000000 47500000 AAB 3
And got the following:
docker-example % docker run --rm
-v $(pwd):/src
-it suluxan/bamgineer-v2
-config /src/inputs/config.cfg
-splitbamdir src/splitbams
-cnv_bed /src/inputs/cnv.new.bed
-vcf src/inputs/normal_het.vcf
-exons src/inputs/exons.bed
-outbam tumour.bam
-results src/outputs
-cancertype LUAC1
('OPTIONS:', Namespace(cancerType='LUAC1', chrList=None, cnvBed='/src/inputs/cnv.new.bed', configfile='/src/inputs/config.cfg', ctDNA=False, exons='src/inputs/exons.bed', inbamFile=None, outBamFile='tumour.bam', outputDir='src/outputs', phase=False, singleXY=False, splitbams='src/splitbams', vcf='src/inputs/normal_het.vcf'))
src/outputs
___ generating phased bed ___
___ filtering bed file columns for gainAAB47000000_tmp2.bed ___
___ extracting roi bams ___
___ splitting original bam into hap1 and hap2 ___
___ re-pairing hap1 bam reads ___
___ removing repaired duplicates ___
finding positions of the duplicate reads in the file...
sorting 49824 end pairs... done in 10 ms
sorting 626441 single ends (among them 622276 unmatched pairs)... done in 26 ms
collecting virtual offsets of duplicate reads... done in 5 ms
found 10279 duplicates, sorting the list... done in 0 ms
collected list of positions in 0 min 5 sec
removing duplicates...
total time elapsed: 0 min 8 sec
___ re-pairing hap2 bam reads ___
___ removing repaired duplicates ___
finding positions of the duplicate reads in the file...
sorting 49383 end pairs... done in 11 ms
sorting 620508 single ends (among them 616064 unmatched pairs)... done in 28 ms
collecting virtual offsets of duplicate reads... done in 6 ms
found 10196 duplicates, sorting the list... done in 0 ms
collected list of positions in 0 min 5 sec
removing duplicates...
total time elapsed: 0 min 8 sec
sambamba-merge: Error reading BGZF block starting from offset 15187326: wrong BGZF magic
sambamba-merge: Error reading BGZF block starting from offset 15167255: wrong BGZF magic
___ removing hap1 merged normal duplicates ___
finding positions of the duplicate reads in the file...
sorting 84909 end pairs... done in 11 ms
sorting 573252 single ends (among them 572403 unmatched pairs)... done in 22 ms
collecting virtual offsets of duplicate reads... done in 7 ms
found 18344 duplicates, sorting the list... done in 0 ms
collected list of positions in 0 min 5 sec
removing duplicates...
total time elapsed: 0 min 8 sec
___ removing hap2 merged normal duplicates ___
finding positions of the duplicate reads in the file...
sorting 85143 end pairs... done in 10 ms
sorting 569723 single ends (among them 568810 unmatched pairs)... done in 28 ms
collecting virtual offsets of duplicate reads... done in 6 ms
found 18035 duplicates, sorting the list... done in 1 ms
collected list of positions in 0 min 5 sec
removing duplicates...
total time elapsed: 0 min 8 sec
___ extracting non-roi bams ___
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
Killed

[suluxan]

Hello,

Sorry for the late reply - likely this is a memory issue!