ryanlayer
commented
4 years ago Are those all of the scaffolds?
On Thu, Sep 5, 2019 at 9:56 AM sofieobr notifications@github.com wrote:
Hi,
I have run lumpyexpress on 24 BWA-MEM mapped sequencing files, all aligned to the same genome. In 2 out of 24 of the samples, lumpy is giving a segmentation fault. The fault occurs at the same scaffold in both files, and lumpy gives a partial output that stops at that scaffold. In the other 22 samples, lumpy ran correctly with no errors. I tried to re-run lumpy, and the same segmentation fault occurs every time, at the same place. I processed all 24 files identically, and had plenty of storage and ram (I ran it with 93GB of ram at one point, and it still had the same error occur). I ran the following lumpyexpress command:
/home/huws/bluvs002/lumpy-sv/bin/lumpyexpress -B "CHOK1_SF_unique_sorted_dup_RG.bam" -S "CHOK1_SF_splitters.bam" -D "CHOK1_SF_discordants.bam" -k -v -T temp -o "CHOK1_SF_lumpy2.vcf"
Even though I used the -k option, all of the temporary files were deleted as soon as the segmentation fault occurred.
Here is the output of lumpy:
Sourcing executables from /home/huws/bluvs002/lumpy-sv/bin/lumpyexpress.config ...
Checking for required python modules (/home/huws/bluvs002/mypython2.7/bin/python2)...
create temporary directoryCalculating insert distributions... Library read groups: 1 Library read length: 90 done 0 Running LUMPY...
/panfs/roc/groups/13/huws/bluvs002/lumpy-sv//bin/lumpy \ -t temp/CHOK1_SF_lumpy2.vcf \ -msw 4 \ -tt 0 \ \ \ -pe bam_file:CHOK1_SF_discordants.bam,histo_file:temp/CHOK1_SF_lumpy2.vcf.sample1.lib1.x4.histo, mean:474.955262533,stdev:38.2016793044,read_length:90,min_non_overlap:90,discordant_z:5,back_distance:10,weight:1,id:CHOK1_SF,min_mapping_threshold:20,read_group:1 \ -sr bam_file:CHOK1_SF_splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:CHOK1_SF,min_clip:20 \
CHOK1_SF_lumpy2.vcf
Here is the error output:
Removed 297 outliers with isize >= 550 470 0 NW_020822366.1 1000000 NW_020822368.1 1000000 NW_020822369.1 1000000 NW_020822370.1 1000000 NW_020822371.1 1000000 NW_020822372.1 1000000 NW_020822373.1 1000000 NW_020822374.1 1000000 NW_020822375.1 1000000 NW_020822376.1 1000000 NW_020822377.1 1000000 NW_020822379.1 1000000 NW_020822380.1 1000000 NW_020822381.1 1000000 NW_020822382.1 1000000 NW_020822383.1 1000000 NW_020822385.1 1000000 NW_020822387.1 1000000 NW_020822388.1 1000000 NW_020822390.1 1000000 NW_020822391.1 1000000 NW_020822393.1 1000000 NW_020822394.1 1000000 NW_020822395.1 1000000 NW_020822396.1 1000000 NW_020822398.1 1000000 NW_020822399.1 1000000 NW_020822400.1 1000000 NW_020822401.1 1000000 NW_020822402.1 1000000 NW_020822403.1 1000000 /home/huws/bluvs002/lumpy-sv/bin/lumpyexpress: line 548: 74238 Segmentation fault (core dumped) $LUMPY $PROB_CURVE -t ${TEMP_DIR}/${OUTBASE} -msw $MIN_SAMPLE_WEIGHT -tt $TRIM_THRES $LUMPY_DEPTH_STRING $EXCLUDE_BED_FMT $LUMPY_DISC_STRING $EXCLUDE_BED_FMT $LUMPY_SPL_STRING > $OUTPUT
Do you know what the problem may be?
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sofieobr
linfeng0204
Hi,
I have run lumpyexpress on 24 BWA-MEM mapped sequencing files, all aligned to the same genome. In 2 out of 24 of the samples, lumpy is giving a segmentation fault. The fault occurs at the same scaffold in both files, and lumpy gives a partial output that stops at that scaffold. In the other 22 samples, lumpy ran correctly with no errors. I tried to re-run lumpy, and the same segmentation fault occurs every time, at the same place. I processed all 24 files identically, and had plenty of storage and ram (I ran it with 93GB of ram at one point, and it still had the same error occur). I ran the following lumpyexpress command:
Even though I used the -k option, all of the temporary files were deleted as soon as the segmentation fault occurred.
Here is the output of lumpy:
Here is the error output:
Do you know what the problem may be?