Segmentation fault problem about angsd

[ANGSD]

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?

[dmvelasco]

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!

[dmvelasco]

Seems to have worked, a non-empty .saf.idx was produced and no segfault.
Thanks again for your help!

[SIlviaHinojosa]

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!

[ANGSD]

It seems to work for my bamfiles: [fvr124@a00643 angsd]$ ./angsd -nThreads 1 -doglf 2 -doMajorMinor 1 -GL 1 -P 5 -doMaf 2 -SNP_pval 2e-6 -checkBamHeaders 0 -bam list -r 1 -> angsd version: 0.917-37-g21acca9-dirty (htslib: 1.3.2-225-g8dd26ff) build(Feb 24 2017 11:22:41) -> No '-out' argument given, output files will be called 'angsdput' -> SNP-filter using a pvalue: 2.000000e-06 correspond to 22.595043 likelihood units -> Parsing 33 number of samples -> Region lookup 1/1 -> Printing at chr: 1 pos:14086716 chunknumber 300 contains 251 sites -> Done reading data waiting for calculations to finish -> Done waiting for threads -> Output filenames: ->"angsdput.arg" ->"angsdput.beagle.gz" ->"angsdput.mafs.gz" -> Tue Mar 7 09:46:48 2017 -> Arguments and parameters for all analysis are located in .arg file [ALL done] cpu-time used = 37.65 sec [ALL done] walltime used = 10.00 sec What is the difference in header, since you are using the -checkbamheaders 0?

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On Mon, Mar 6, 2017 at 12:52 PM, SIlviaHinojosa ***@***.***> wrote: 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! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#13 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGDo7qx_ha9SfP0YyR0EOBwm2SXj4-lZks5ri_OMgaJpZM4EcZNr> .

[SIlviaHinojosa]

Hello This are my headers of two of the samples : @hd VN:1.0 SO:coordinate @sq SN:comp0_seq0 LN:5714 @hd VN:1.0 SO:coordinate @sq SN:comp0 LN:5219 I have tried to run it without checking bam headers and I got an error that headers were different, then I ran it with the checkbam and worked, then I added this two samples and It didn worked any more. I was using the program just fine for the last couple of weeks and then this error started. Silvia 2017-03-07 9:48 GMT+01:00 ANGSD <[email protected]>:

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It seems to work for my bamfiles: ***@***.*** angsd]$ ./angsd -nThreads 1 -doglf 2 -doMajorMinor 1 -GL 1 -P 5 -doMaf 2 -SNP_pval 2e-6 -checkBamHeaders 0 -bam list -r 1 -> angsd version: 0.917-37-g21acca9-dirty (htslib: 1.3.2-225-g8dd26ff) build(Feb 24 2017 11:22:41) -> No '-out' argument given, output files will be called 'angsdput' -> SNP-filter using a pvalue: 2.000000e-06 correspond to 22.595043 likelihood units -> Parsing 33 number of samples -> Region lookup 1/1 -> Printing at chr: 1 pos:14086716 chunknumber 300 contains 251 sites -> Done reading data waiting for calculations to finish -> Done waiting for threads -> Output filenames: ->"angsdput.arg" ->"angsdput.beagle.gz" ->"angsdput.mafs.gz" -> Tue Mar 7 09:46:48 2017 -> Arguments and parameters for all analysis are located in .arg file [ALL done] cpu-time used = 37.65 sec [ALL done] walltime used = 10.00 sec What is the difference in header, since you are using the -checkbamheaders 0? On Mon, Mar 6, 2017 at 12:52 PM, SIlviaHinojosa ***@***.***> wrote: > 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! > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#13 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AGDo7qx_ ha9SfP0YyR0EOBwm2SXj4-lZks5ri_OMgaJpZM4EcZNr> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#13 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AZAeEo2TWodwWIE47YfZ0Rxack5ik4oJks5rjRnPgaJpZM4EcZNr> .

[ANGSD]

It looks like your bams dont cover the same chromosomes? If things keep crashing then try reformatting your bams so they have identical headers. On Tue, Mar 7, 2017 at 10:19 AM, SIlviaHinojosa <[email protected]> wrote:

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Hello This are my headers of two of the samples : @hd VN:1.0 SO:coordinate @sq SN:comp0_seq0 LN:5714 @hd VN:1.0 SO:coordinate @sq SN:comp0 LN:5219 I have tried to run it without checking bam headers and I got an error that headers were different, then I ran it with the checkbam and worked, then I added this two samples and It didn worked any more. I was using the program just fine for the last couple of weeks and then this error started. Silvia 2017-03-07 9:48 GMT+01:00 ANGSD ***@***.***>: > It seems to work for my bamfiles: > > ***@***.*** angsd]$ ./angsd -nThreads 1 -doglf 2 -doMajorMinor 1 -GL 1 > -P 5 -doMaf 2 -SNP_pval 2e-6 -checkBamHeaders 0 -bam list -r 1 > > -> angsd version: 0.917-37-g21acca9-dirty (htslib: 1.3.2-225-g8dd26ff) > build(Feb 24 2017 11:22:41) > > -> No '-out' argument given, output files will be called 'angsdput' > > -> SNP-filter using a pvalue: 2.000000e-06 correspond to 22.595043 > likelihood units > > -> Parsing 33 number of samples > > -> Region lookup 1/1 > > -> Printing at chr: 1 pos:14086716 chunknumber 300 contains 251 sites > > -> Done reading data waiting for calculations to finish > > -> Done waiting for threads > > -> Output filenames: > > ->"angsdput.arg" > > ->"angsdput.beagle.gz" > > ->"angsdput.mafs.gz" > > -> Tue Mar 7 09:46:48 2017 > > -> Arguments and parameters for all analysis are located in .arg file > > [ALL done] cpu-time used = 37.65 sec > > [ALL done] walltime used = 10.00 sec > > > What is the difference in header, since you are using the -checkbamheaders > 0? > > On Mon, Mar 6, 2017 at 12:52 PM, SIlviaHinojosa < ***@***.***> > wrote: > > > 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! > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > <#13 (comment)>, or > mute > > the thread > > <https://github.com/notifications/unsubscribe-auth/AGDo7qx_ > ha9SfP0YyR0EOBwm2SXj4-lZks5ri_OMgaJpZM4EcZNr> > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#13 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ AZAeEo2TWodwWIE47YfZ0Rxack5ik4oJks5rjRnPgaJpZM4EcZNr> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#13 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGDo7tGIj2jE03pNRoNwSIhlapYWQwiFks5rjSEsgaJpZM4EcZNr> .