Pindel :: terminate called after throwing an instance of 'std::out_of_range'

Question

[Wai Yi Leung]

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

[Sam]

There is no bam index?

[Wai Yi Leung]

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?