Comments (7)
The -doSaf was moved to a more intelligent container format in the latests version. Maybe a bug managed to sneak in. I can see that it crashes when it tries to close the files.
Is it a big scaffold? Would it take long to reproduce the segfault? I Just pushed a new version to github could you try rerun with that?
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Excellent! I'll give it a try. It is a tiny genome, comparatively, at ~230 Mb with the first chromosome being the largest at ~48 Mb. While I didn't time it exactly, it was around an hour to finish. I will let you know how it goes. Thanks for your help!
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Seems to have worked, a non-empty .saf.idx was produced and no segfault.
Thanks again for your help!
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Hello
I am having the same problem : Parsing 7 number of samples
Segmentation fault (core dumped) . I am using the latest angsd version and tried diferent -nThreads 1,10,20 etc ... here is the comand line.
/angsd -out /user/shinojosa/bams/Dysdera_all/banda_all_out -nThreads 1 -doGlf 2 -doMajorMinor 1 -GL 1 -P 5 -doMaf 2 -SNP_pval 2e-6 -checkBamHeaders 0 -bam /user/shinojosa/bams/Dysdera_all/bam_banda.filelist
Thanks!
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Related Issues (20)
- Segmentation Fault HOT 1
- problems with estAvgError.R HOT 1
- Length of fastafile vs length of chr in BAM header HOT 1
- Contamination test, Error in dimnames(x)
- Population level theta with saf2theta
- [loadChr] Error loading fasta info from chr
- Missing windows in thetaStat
- Number of numbers output by realSFS HOT 1
- merging binary all 10 log genotype likelihood
- angsd: realloc() error
- 0 sites retained after filtering when using -sites HOT 1
- estAvgError.R script error
- -argument is unknown will exit HOT 1
- Killed HOT 1
- Problems with unsorted saf file chromoname HOT 1
- SAF file out of sync
- bcf file doesn't open
- https://www.popgen.dk/angsd/ is down
- bcf output file with "." at QUAL column
- Issue with angsd -doSaf 1 Not Generating Proper saf.idx File
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