Pindel Segmentation Fault Error

Question

[Yuelin]

Hi all,

I am new in using pindel. Recently I always get Segmentation fault error with pindel 0.2.5a3 (Oct 24 2013) when process large files (whole genome) and your insights will be greatly appreciated.

This is the command I used:

$ echo "Tumor.realigned.md.bam 170 test" > Tumor.txt
$ pindel  -T 16 -f ucsc.hg19.fasta -i Tumor.txt -c ALL -o Tumor.pdl

This is the error message:

/bin/bash: line 1: 20276 Segmentation fault     pindel  -T 16 -f ucsc.hg19.fasta -i Tumor.txt -c ALL -o Tumor.pdl

Jack

[Danielk]

For some samples, I have the same problem. My files are generated with bwa mem.

tools/pindel -f /mnt/hds/proj/cust001/autoseq_genome/genome/human_g1k_v37_decoy.fasta -i /mnt/hds/proj/cust001/analyzed/L5306/L5306T-L5306N.pindelconfig -o /mnt/hds/proj/cust001/analyzed/L530/L5306T-L5306N.pindel

The pindel config file:

/mnt/hds/proj/cust001/analyzed/L5306/clinseq_v1/L5306T.bam    250    L5306T
/mnt/hds/proj/cust001/analyzed/L5306/clinseq_v1/L5306N.bam    250    L5306N

It runs for a while, then dies, saying

Searching deletion-insertions ...
Total: 9195     +4736   -4459
Sorting and outputing deletions with non-template sequences ...
Added: Sorting and outputing deletions with non-template sequences ...
deletions with non-template sequences: 56

Searching tandem duplication events ...
/mnt/hds/proj/cust001/tmp/.exec3703140885509234414: line 2: 39349 Segmentation fault      tools/pindel -f /mnt/hds/proj/cust001/autoseq_genome/genome/human_g1k_v37_decoy.fasta -i /mnt/hds/proj/cust001/analyzed/L5306/clinseq_v1/L5306T-L5306N.pindelconfig -o /mnt/hds/proj/cust001/analyzed/L5306/clinseq_v1/L5306T-L5306N.pindel

I'm using pindel 0.2.5a3, Oct 24 2013. @liangkaiye, any ideas?

Daniel

[RT]

This the tool still problematic?