Segmentation fault with Lumpy

Hi,

I am testing Lumpy over WGS data (50X, 150bp PE; with only chr22) and got the error message of segmentation fault (please see below). Not sure where the error came though the output vcf file was created for few CNVs. The bam files were generated by bwa-mem as suggested.

Thanks

Joon

$ lumpyexpress -B TEST0089.final.chr22.bam -S TEST0089.final.chr22.splitters.bam -D TEST0089.final.chr22.discordants.bam -o test1.vcf -v Sourcing executables from /usr/local/bin/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)...

create temporary directory

Calculating insert distributions... Library read groups: TEST0089_TCTCGCGC_H00W9ALXX_L003,TEST0089_TCTCGCGC_H00WMALXX_L005 Library read length: 151 Removed 3 outliers with isize >= 909 done 0 Running LUMPY...

/opt/software/lumpy-sv//bin/lumpy \ -t test1.vcf.QTycwNRnEtuh/test1.vcf \ -msw 4 \ -tt 0 \ \ -pe bam_file:TEST0089.final.chr22.discordants.bam,histo_file:test1.vcf.QTycwNRnEtuh/test1.vcf.sample1.lib1.x4.histo,mean:363.965294502,stdev:81.2851183648,read_length:151,min_non_overlap:151,discordant_z:5,back_distance:10,weight:1,id:TEST0089,min_mapping_threshold:20,read_group:TEST0089_TCTCGCGC_H00W9ALXX_L003,read_group:TEST0089_TCTCGCGC_H00WMALXX_L005 \ -sr bam_file:TEST0089.final.chr22.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:TEST0089,min_clip:20 \

test1.vcf 22 1000000 22 2000000 22 4000000 22 8000000 22 16000000 22 32000000 /usr/local/bin/lumpyexpress: line 411: 35762 Segmentation fault $LUMPY $PROB_CURVE -t ${TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES $EXCLUDE_BED_FMT $LUMPY_DISC_STRING $LUMPY_SPL_STRING > $OUTPUT

hall-lab / speedseq

Segmentation fault with Lumpy #65