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mobinasri / secphase

Phasing reads with secondary alignments
MIT License
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v0.4.3 core dump #11

Open ptrebert opened 1 year ago

ptrebert commented 1 year ago

Hi, I am running v0.4.3 as a Singularity container. secphase_index can process the BAM file (1 cell of hifi reads), but when I start secphase like this:

./secphase_v0.4.3.sif secphase -i sample.nsort.bam -f sample.fasta --hifi

it immediately segfaults (the index is present in the same folder named like sample.bam.secphase.index). In principle, I could share the BAM file for debugging if required, but only via Globus.

Best, Peter

mobinasri commented 1 year ago

@ptrebert

Sorry for the late response. v0.4.3 does not need indexing anymore but indexing shouldn't be related to that segfault. Could you please share the BAM and fasta file?