Entering edit mode
4.3 years ago
amyruthvandiver
•
0
Hello, I have been trying to run pindel on MiSeq data of mitochondrial genome amplicon data and repeatedly receive a segmentation error I have not been able to trouble shoot. I do not have this error with the demo files and can run those without issue. I am running pindel using a bam file aligned with BWA, using the reference genome used for alignment. I have tried trouble shooting per the pindel user guide and a prior thread from 2013:
- I have tried running on small downsampled file to make sure it is not a memory issue, this did not help
- I have tried running sam2pindel on the input and get the same issue when I run that
- I am using pindel 0.2.5b8, installed via anaconda
Below is the error I get:
pindel -f sequence.fasta -i jwtest/config.txt -c M -o output/jw
Initializing parameters...
Pindel version 0.2.5b8, 20151210.
Loading reference genome ...
Loading reference genome done.
Initializing parameters done.
SearchRegion::SearchRegion
Segmentation fault: 11
Thank you for any guidance!
