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Published 20 hours ago • verified publisher icon COMBINE-lab

Pairwise IBD Computations - Segmentation fault

Open alizraksi opened this issue 5 years ago • 0 comments

I get the following error when trying to run lcMLkin:

$ ~/apps/maximum-likelihood-relatedness-estimation/lcmlkin -i targeted.thinned.recode.vcf -o pairwise.relate.txt -g all -t 8
lcMLkin v0.5.0
==============================
using 8 threads
Populating Data
[2019-05-09 11:43:00.029] [jointLog] [info] Genotype likelihood format is RAW
[2019-05-09 11:43:00.059] [jointLog] [info] Parsed variants at 19 total sites
[2019-05-09 11:43:00.059] [j
[targeted.thinned.recode.head5.vcf.txt](https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation/files/3163599/targeted.thinned.recode.head5.vcf.txt)
[targeted.thinned.recode.head5.vcf.txt](https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation/files/3163603/targeted.thinned.recode.head5.vcf.txt)
[targeted.thinned.recode.head5.vcf.txt](https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation/files/3163605/targeted.thinned.recode.head5.vcf.txt)


ointLog] [info] allele freqs = 19
[2019-05-09 11:43:00.059] [jointLog] [info] gt likelihoods = 19
number of SNPs masked (freq 0) = 0
number of SNPs masked (freq 1) = 0
Calculating Prestored IBS|IBD
Starting Pairwise IBD Computations
Segmentation fault (core dumped)

Is there a way to debug this? I'm trying to compare 518 samples, and I generated the VCF file using SNPbam2vcf.py. Here's a subset of the VCF file, in case it helps:

##Custom variant caller for_lcMLkin
##Bayesian_caller=0,MappingQuality_filter=20,BaseQuality_filter=5,GenotypeQuality_filter=0.1,bamlist=/home/arao/toca5/relatedness/phase2retest/bam_list.wphase2retest.txt,filenameout=/home/arao/toca5/relatedness/phase2retest/toca5_bams_merged.targeted.wphase2retest.vcf,SNPfile=/home/arao/toca5/relatedness/00-common_all.noindels.chr.targeted.fewcols.singlebase.vcf
##Time created: 13:37:27 01/05/2019
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	IM098B_S3_001	IM098T_S7_001	IM113B_S1_001	IM113T_S5_001	IM137B_S3_001	IM137T_S7_001	IM323B_S2_001	IM323T_S6_001	IM384B_S2_001	IM384T_S6_001	IM480B_S2_001	IM480T_S6_001	IM399B_S1_001	IM399T_S5_001	IM460B_S3_001	IM460T_S7_001	IM039B_S3_001	IM039T_S7_001	IM056B_S4_001	IM056T_S8_001	IM136B_S2_001	IM136T_S6_001	IM243B_S2_001	IM243T_S6_001	IM001B_S1_001	IM001T_S5_001	IM010B_S3_001	IM010T_S7_001	IM067B_S1_001	IM067T_S5_001	IM072B_S3_001	IM072T_S7_001	IM069B_S2_001	IM069T_S6_001	IM166B_S4_001	IM166T_S8_001	IM168B_S1_001	IM168T_S5_001	IM190B_S4_001	IM190T_S8_001	IM195B_S2_001	IM195T_S6_001	IM246B_S3_001	IM246T_S7_001	IM491B_S4_001	IM491T_S8_001	IM103B_S4_001	IM103T_S8_001	IM163B_S3_001	IM163T_S7_001	IM233B_S3_001	IM233T_S7_001	IM359B_S1_001	IM359T_S5_001	IM108B_S3_001	IM108T_S7_001	IM374B_S2_001	IM374T_S6_001	IM228B_S2_001	IM228T_S6_001	IM237B_S1_001	IM237T_S5_001	IM258B_S3_001	IM258T_S7_001	IM304B_S2_001	IM304T_S6_001	IM348B_S3_001	IM348T_S7_001	IM280B_S4_001	IM280T_S8_001	IM502B_S4_001	IM502T_S8_001	IM319B_S4_001	IM319T_S8_001	IM006B_S2_001	IM006T_S6_001	IM202B_S4_001	IM202T_S8_001	IM259B_S4_001	IM259T_S8_001	IM045B_S4_001	IM045T_S8_001	IM065B_S4_001	IM065T_S8_001	IM064B_S3_001	IM064T_S7_001	IM161B_S2_001	IM161T_S6_001	IM271B_S2_001	IM271T_S6_001	IM347B_S2_001	IM347T_S6_001	IM208B_S3_001	IM208T_S7_001	IM049B_S2_001	IM049T_S6_001	IM024B_S3_001	IM024T_S7_001	IM201B_S1_001	IM201T_S5_001	IM288B_S1_001	IM288T_S5_001	IM032B_S1_001	IM032T_S5_001	IM205B_S2_001	IM205T_S6_001	IM295B_S3_001	IM295T_S7_001	IM158B_S3_001	IM158T_S7_001	IM182B_S3_001	IM182T_S7_001	IM253B_S2_001	IM253T_S6_001	IM282B_S3_001	IM282T_S7_001	IM335B_S2_001	IM335T_S6_001	IM395B_S4_001	IM395T_S8_001	IM421B_S4_001	IM421T_S8_001	IM012B_S3_001	IM012T_S7_001	IM025B_S4_001	IM025T_S8_001	IM037B_S2_001	IM037T_S6_001	IM251B_S1_001	IM251T_S5_001	IM456B_S1_001	IM456T_S5_001	IM173B_S2_001	IM173T_S6_001	IM252B_S2_001	IM252T_S6_001	IM292B_S2_001	IM292T_S6_001	IM379B_S3_001	IM379T_S7_001	IM426B_S2_001	IM426T_S6_001	IM149B_S1_001	IM149T_S5_001	IM504B_S1_001	IM504T_S5_001	IM128B_S2_001	IM128T_S6_001	IM424B_S2_001	IM424T_S6_001	IM048B_S1_001	IM048T_S5_001	IM106B_S2_001	IM106T_S6_001	IM224B_S1_001	IM224T_S5_001	IM030B_S1_001	IM030T_S5_001	IM044B_S2_001	IM044T_S6_001	IM109B_S4_001	IM109T_S8_001	IM131B_S4_001	IM131T_S8_001	IM152B_S2_001	IM152T_S6_001	IM234B_S4_001	IM234T_S8_001	IM329B_S1_001	IM329T_S5_001	IM404B_S2_001	IM404T_S6_001	IM266B_S1_001	IM266T_S5_001	IM392B_S4_001	IM392T_S8_001	IM412B_S2_001	IM412T_S6_001	IM020B_S4_001	IM020T_S8_001	IM086B_S1_001	IM086T_S5_001	IM415B_S3_001	IM415T_S7_001	IM350B_S4_001	IM350T_S8_001	IM009B_S2_001	IM009T_S6_001	IM213B_S4_001	IM213T_S8_001	IM413B_S4_001	IM413T_S8_001	IM486B_S3_001	IM486T_S7_001	IM139B_S1_001	IM139T_S5_001	IM197B_S3_001	IM197T_S7_001	IM242B_S1_001	IM242T_S5_001	IM425B_S1_001	IM425T_S5_001	IM420B_S1_001	IM420T_S5_001	IM483B_S3_001	IM483T_S7_001	IM466B_S1_001	IM466T_S5_001	IM435B_S3_001	IM435T_S7_001	IM411B_S3_001	IM411T_S7_001	IM451B_S2_001	IM451T_S6_001	IM442B_S4_001	IM442T_S8_001	IM450B_S1_001	IM450T_S5_001	IM345B_S4_001	IM345T_S8_001	IM200B_S4_001	IM200T_S8_001	IM219B_S3_001	IM219T_S7_001	IM104B_S1_001	IM104T_S5_001	IM147B_S4_001	IM147T_S8_001	IM218B_S2_001	IM218T_S6_001	IM318B_S1_001	IM318T_S5_001	IM360B_S1_001	IM360T_S5_001	IM314B_S3_001	IM314T_S7_001	IM387B_S3_001	IM387T_S7_001	IM051B_S3_001	IM051T_S7_001	IM130B_S3_001	IM130T_S7_001	IM191B_S1_001	IM191T_S5_001	IM223B_S4_001	IM223T_S8_001	IM247B_S4_001	IM247T_S8_001	IM287B_S1_001	IM287T_S5_001	IM315B_S4_001	IM315T_S8_001	IM332B_S3_001	IM332T_S7_001	IM479B_S2_001	IM479T_S6_001	IM016B_S4_001	IM016T_S8_001	IM022B_S2_001	IM022T_S6_001	IM027B_S1_001	IM027T_S5_001	IM116B_S2_001	IM116T_S6_001	IM120B_S3_001	IM120T_S7_001	IM121B_S4_001	IM121T_S8_001	IM487B_S4_001	IM487T_S8_001	IM083B_S4_001	IM083T_S8_001	IM090B_S2_001	IM090T_S6_001	IM094B_S3_001	IM094T_S7_001	IM123B_S1_001	IM123T_S5_001	IM274B_S3_001	IM274T_S7_001	IM122B_S4_001	IM122T_S8_001	IM133B_S1_001	IM133T_S5_001	IM397B_S1_001	IM397T_S5_001	IM217B_S1_001	IM217T_S5_001	IM455B_S4_001	IM455T_S8_001	IM492B_S1_001	IM492T_S5_001	IM440B_S3_001	IM440T_S7_001	IM464B_S4_001	IM464T_S8_001	IM098B_S3_001	IM098T_S7_001	IM113B_S1_001	IM113T_S5_001	IM137B_S3_001	IM137T_S7_001	IM323B_S2_001	IM323T_S6_001	IM384B_S2_001	IM384T_S6_001	IM480B_S2_001	IM480T_S6_001	IM460B_S3_001	IM460T_S7_001	IM039B_S3_001	IM039T_S7_001	IM056B_S4_001	IM056T_S8_001	IM136B_S2_001	IM136T_S6_001	IM001B_S1_001	IM001T_S5_001	IM010B_S3_001	IM010T_S7_001	IM067B_S1_001	IM067T_S5_001	IM072B_S3_001	IM072T_S7_001	IM069B_S2_001	IM069T_S6_001	IM168B_S1_001	IM168T_S5_001	IM246B_S3_001	IM246T_S7_001	IM491B_S4_001	IM491T_S8_001	IM103B_S4_001	IM103T_S8_001	IM163B_S3_001	IM163T_S7_001	IM233B_S3_001	IM233T_S7_001	IM359B_S1_001	IM359T_S5_001	IM108B_S3_001	IM108T_S7_001	IM374B_S2_001	IM374T_S6_001	IM237B_S1_001	IM237T_S5_001	IM304B_S2_001	IM304T_S6_001	IM348B_S3_001	IM348T_S7_001	IM280B_S4_001	IM280T_S8_001	IM319B_S4_001	IM319T_S8_001	IM259B_S4_001	IM259T_S8_001	IM065B_S4_001	IM065T_S8_001	IM064B_S3_001	IM064T_S7_001	IM271B_S2_001	IM271T_S6_001	IM347B_S2_001	IM347T_S6_001	IM208B_S3_001	IM208T_S7_001	IM201B_S1_001	IM201T_S5_001	IM288B_S1_001	IM288T_S5_001	IM205B_S2_001	IM205T_S6_001	IM295B_S3_001	IM295T_S7_001	IM158B_S3_001	IM158T_S7_001	IM182B_S3_001	IM182T_S7_001	IM253B_S2_001	IM253T_S6_001	IM282B_S3_001	IM282T_S7_001	IM335B_S2_001	IM335T_S6_001	IM395B_S4_001	IM395T_S8_001	IM421B_S4_001	IM421T_S8_001	IM012B_S3_001	IM012T_S7_001	IM456B_S1_001	IM456T_S5_001	IM173B_S2_001	IM173T_S6_001	IM292B_S2_001	IM292T_S6_001	IM426B_S2_001	IM426T_S6_001	IM149B_S1_001	IM149T_S5_001	IM504B_S1_001	IM504T_S5_001	IM128B_S2_001	IM128T_S6_001	IM424B_S2_001	IM424T_S6_001	IM048B_S1_001	IM048T_S5_001	IM106B_S2_001	IM106T_S6_001	IM030B_S1_001	IM030T_S5_001	IM109B_S4_001	IM109T_S8_001	IM131B_S4_001	IM131T_S8_001	IM152B_S2_001	IM152T_S6_001	IM234B_S4_001	IM234T_S8_001	IM329B_S1_001	IM329T_S5_001	IM404B_S2_001	IM404T_S6_001	IM266B_S1_001	IM266T_S5_001	IM392B_S4_001	IM392T_S8_001	IM412B_S2_001	IM412T_S6_001	IM020B_S4_001	IM020T_S8_001	IM415B_S3_001	IM415T_S7_001	IM350B_S4_001	IM350T_S8_001	IM009B_S2_001	IM009T_S6_001	IM413B_S4_001	IM413T_S8_001	IM486B_S3_001	IM486T_S7_001	IM139B_S1_001	IM139T_S5_001	IM197B_S3_001	IM197T_S7_001	IM242B_S1_001	IM242T_S5_001	IM420B_S1_001	IM420T_S5_001	IM483B_S3_001	IM483T_S7_001	IM435B_S3_001	IM435T_S7_001	IM411B_S3_001	IM411T_S7_001	IM451B_S2_001	IM451T_S6_001	IM442B_S4_001	IM442T_S8_001	IM450B_S1_001	IM450T_S5_001	IM200B_S4_001	IM200T_S8_001	IM219B_S3_001	IM219T_S7_001	IM104B_S1_001	IM104T_S5_001	IM147B_S4_001	IM147T_S8_001	IM218B_S2_001	IM218T_S6_001	IM318B_S1_001	IM318T_S5_001	IM314B_S3_001	IM314T_S7_001	IM387B_S3_001	IM387T_S7_001	IM051B_S3_001	IM051T_S7_001	IM130B_S3_001	IM130T_S7_001	IM223B_S4_001	IM223T_S8_001	IM247B_S4_001	IM247T_S8_001	IM287B_S1_001	IM287T_S5_001	IM315B_S4_001	IM315T_S8_001	IM479B_S2_001	IM479T_S6_001	IM016B_S4_001	IM016T_S8_001	IM022B_S2_001	IM022T_S6_001	IM121B_S4_001	IM121T_S8_001	IM083B_S4_001	IM083T_S8_001	IM090B_S2_001	IM090T_S6_001	IM123B_S1_001	IM123T_S5_001	IM274B_S3_001	IM274T_S7_001	IM122B_S4_001	IM122T_S8_001	IM133B_S1_001	IM133T_S5_001	IM397B_S1_001	IM397T_S5_001	IM217B_S1_001	IM217T_S5_001	IM492B_S1_001	IM492T_S5_001	IM464B_S4_001	IM464T_S8_001
chr1	13273	.	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I've run lcMLkin successfully previously with a different dataset but have upgraded the OS (currently Ubuntu 18.04) since then. I tried reinstalling lcMLkin but for some reason I'm getting an error now, when running make. It gets as far as:

src/Variant.cpp: In member function ‘double vcflib::Variant::getSampleValueFloat(std::__cxx11::string&, st d::__cxx11::string&, int)’:
src/Variant.cpp:404:5: warning: control reaches end of non-void function [-Wreturn-type]
     }
     ^
Makefile:12: recipe for target 'lcmlkin' failed
make: *** [lcmlkin] Error 1

Thanks ahead for any help!

alizraksi avatar May 09 '19 19:05 alizraksi