Question: Pindel :: terminate called after throwing an instance of 'std::out_of_range'
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gravatar for Wai Yi Leung
22 months ago by
Wai Yi Leung30
Netherlands
Wai Yi Leung30 wrote:

I've some difficulties running Pindel on a WGS bam (human genome GRCh38). I've no problems running pindel on bacteria samples i have (with same settings).

The program crashes with the following message:

======

BAM file index  0
Bam file name   /data/700232000002.dedup.realign.bam
Number of split-reads so far    197901

The number of one end mapped read: 197901
There are 1507751 reads supporting the reference allele.
There are 1 samples.
SampleName2Index done
declaring g_RefCoverageRegion for 1 samples and 5000001 positions.
There are 197901 split-reads for this chromosome region.

There are 0 split-reads mapped by aligner.
search far ends
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::at
/LTstorage/script.sh: line 4: 39014 Aborted                 (core dumped) '/usr/local/pindel/pindel-0.2.5b8/pindel' '--fasta' '/usr/local/Genomes/H.Sapiens/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna' '--config-file' '/LTstorage/700232000002.pindel.cfg' '--output-prefix' '/LTstorage/700232000002/sample' '--number_of_threads' '4'

======

Does anyone recognise the error and is there a fix for this?

 

p.s. Some of the paths shown are replaced to focus on the issue

 

 

pindel software error • 1.1k views
ADD COMMENTlink written 22 months ago by Wai Yi Leung30

There is no bam index?

ADD REPLYlink written 22 months ago by Sam2.1k

The bam has an index.

The issue is solved by using a correct Fasta file. (alignment used an other fasta file)

Maybe this could be added to pindel, to warn a user whenever the supplied reference_fasta is not the same as stated in the header of a bamfile?

ADD REPLYlink written 22 months ago by Wai Yi Leung30
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