std::out_of_range error

[aeonsim]

Hi Erik

We've hit another bug, when running freebayes as below we're getting this error with the build (2f4c924) and the previous couple:

terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Aborted

I've sent you a subset bam that can reproduce the error, It's the same reference as last time.

Thanks
Chad

Command

./freebayes/bin/freebayes -v freebayes-output-0.9.4.vcf -f /data/seq/indexed-genomes/bos_taurus/umd31MT/umd31MT.fa -b /data/seq/processed-genomes/RTG/Denovo/sequence/346_pe_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/664221/sequence/664221_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/664195/sequence/664195_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/99592/sequence/99592_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/99593/sequence/99593_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/99594/sequence/99594_mated.bam -b /data/seq/processed-genomes/RTG/FJXB_Trio/F1-Sire-99591/aligned_sequence/99591_mated.bam -b /data/seq/processed-genomes/RTG/FJXB_Trio/F1-Dam-10841297/aligned_sequence/10841297_mated_v2.bam -b /data/seq/processed-genomes/RTG/FJXB_Trio/F2-Daughter-17144784/aligned_sequence/17144784_mated.bam -b /data/seq/processed-genomes/RTG/Outliers/27/sequence/27_mated.bam -b /data/seq/processed-genomes/RTG/Outliers/363/sequence/363_mated.bam -b /data/seq/processed-genomes/RTG/Outliers/372/sequence/372_mated.bam -b /data/seq/processed-genomes/RTG/Outliers/586/sequence/586_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17074197/sequence/17074197_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17108826/sequence/17108826_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17144783/sequence/17144783_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17145716/sequence/17145716_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18033109/sequence/18033109_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18093560/sequence/18093560_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18143602/sequence/18143602_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18186561/sequence/18186561_mated.bam
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Aborted

-dd Output

---

combo posterior prob: -70.0
{"17074197":["C/I:2983780:1M1I:CG",0.5], "17108826":["C/C",1.0], "17145716":["C/C:2983780:1X1I:GG",0.3], "18033109":["C/C",1.0], "18143602":["C/C",1.0], "18186561":["C/C",1.0], "27":["C/C",1.0], "363":["C/I:2983780:1M1I:CG",0.0], "372":["C/C",1.0], "586":["C/C",1.0], "664195":["C/C",1.0], "664221":["C/C",0.0], "99591":["C/C",1.0], "99592":["C/C",1.0], "99593":["C/C",1.0], "99594":["C/C",1.0]}
combo posterior prob: -80.3
{"17074197":["C/I:2983780:1M1I:CG",0.5], "17108826":["C/C",1.0], "17145716":["C/C:2983780:1X1I:GG",0.3], "18033109":["C/C",1.0], "18143602":["C/C",1.0], "18186561":["C/C",1.0], "27":["C/C",1.0], "363":["C/I:2983780:1M1I:CG",0.0], "372":["C/C",1.0], "586":["C/C",1.0], "664195":["C/C",1.0], "664221":["C/C:2983780:1X1I:GG",0.0], "99591":["C/C",1.0], "99592":["C/C",1.0], "99593":["C/C",1.0], "99594":["C/C",1.0]}
combo posterior prob: -91.5
{"17074197":["C/C",0.0], "17108826":["C/C",1.0], "17145716":["C/C",0.0], "18033109":["C/C",1.0], "18143602":["C/C",1.0], "18186561":["C/C",1.0], "27":["C/C",1.0], "363":["C/C",0.0], "372":["C/C",1.0], "586":["C/C",1.0], "664195":["C/C",1.0], "664221":["C/C",0.0], "99591":["C/C",1.0], "99592":["C/C",1.0], "99593":["C/C",1.0], "99594":["C/C",1.0]}
combo posterior prob: -838.5
{"17074197":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",1.0], "17108826":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "17145716":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "18033109":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "18143602":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "18186561":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "27":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "363":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "372":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "586":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "664195":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "664221":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "99591":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "99592":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "99593":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0], "99594":["I:2983780:1M1I:CG/I:2983780:1M1I:CG",0.0]}
combo posterior prob: -908.4
{"17074197":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "17108826":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "17145716":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "18033109":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "18143602":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "18186561":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "27":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "363":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "372":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "586":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "664195":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "664221":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "99591":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "99592":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "99593":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0], "99594":["C:2983780:1X1I:GG/C:2983780:1X1I:GG",0.0]}
got bestAlleleSamplingProb
pVar = 1.0 0.0 pHom = 0.0 1 - pHom = 1.0
1 - 0.0 >= 0.0
passed PVL threshold
calculating marginal likelihoods
generating banded genotype combinations from 16 sample genotypes in population DEFAULT
best combo: combo posterior prob: -34.3
{"17074197":["C/I:2983780:1M1I:CG",0.5], "17108826":["C/C",1.0], "17145716":["C/C:2983780:1X1I:GG",0.3], "18033109":["C/C",1.0], "18143602":["C/C",1.0], "18186561":["C/C",1.0], "27":["C/C",1.0], "363":["C/I:2983780:1M1I:CG",0.0], "372":["C/C",1.0], "586":["C/C",1.0], "664195":["C/C",1.0], "664221":["C/I:2983780:1M1I:CG",0.0], "99591":["C/C",1.0], "99592":["C/C",1.0], "99593":["C/C",1.0], "99594":["C/C",1.0]}
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr

[chapmanb]

Erik and Chad;
I ran into this problem as well with the current master branch. Here is a reproducible example file with two reads:

$ freebayes -d -b freebayes_problem.bam -v test.vcf -f GRCh37.fa 2> freebayes_debug.out

The BAM file and GRCh37 reference (from Broad):

https://s3.amazonaws.com/chapmanb/freebayes_problem.bam
ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/1.2/b37/human_g1k_v37.fasta.gz

and here is the debug output:

https://s3.amazonaws.com/chapmanb/freebayes_debug.out

Let me know if I can provide any other information that will help.

[ekg]

Please pull. This should be resolved as of 094879e

[andreaswallberg]

I keep hitting this bug as well and I suggest opening it again. The error message I get is:

terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Command terminated by signal 6

This happens for files where I specify the starting and stopping position using the -r switch, such as:

-r Group1:23500000..2399999

Manually rewinding the starting position a few bases fixes the issue for me, so that I for instance start with:

-r Group1:23499990..2399999

This manual tweak is, however, a nightmare when trying to batch run multiple instances in parallel on our cluster automatically...

[ekg]

Hi Andreas,

Could you please send me a test case which causes this issue?
On Aug 8, 2012 4:17 AM, "Andreas Wallberg" notifications@github.com wrote:

I keep hitting this bug as well and I suggest opening it again. The error
message I get is:

terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Command terminated by signal 6

This happens for files where I specify the starting and stopping position
using the -r switch, such as:

-r Group1:23500000..2399999

Manually rewinding the starting position a few bases fixes the issue for
me, so that I for instance start with:

-r Group1:23499990..2399999

This manual tweak is, however, a nightmare when trying to batch run
multiple instances in parallel on our cluster automatically...

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/22#issuecomment-7577758.

[andreaswallberg]

Check you email!