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gymreklab / GangSTR

A tool for profiling long STRs from short reads
GNU General Public License v2.0
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munmap_chunk(): invalid pointer #98

Closed mvcakir closed 3 years ago

mvcakir commented 3 years ago

Hello,

I try to run GangSTR with GRCh38 (version 35) fasta, I use your regions file (hg38_ver13) and it gives this munmap_chunk() error with the first entry already;

ProgressMeter: Processing chr1:10486 munmap_chunk(): invalid pointer Aborted (core dumped)

The bams are generated by bwa mem mapping with the same reference fa of course.

Below is the call;

GangSTR --bam SRR6761495.bam,SRR6761497.bam,SRR6761499.bam --ref GRCh38.p13.v35.genome.fa --regions hg38_ver13.bed --out GangSTR_test

I have no idea what is wrong here.

Thanks for your help already.

Best Regards

nmmsv commented 3 years ago

Hello, Can you please let me know which version of GangSTR you are currently using? And which operating system you are running on? Thanks. Nima

mvcakir commented 3 years ago

Dear Nima,

I'm using GangSTR 2.4 on Fedora 32 (workstation ed.).

Volkan

nmmsv commented 3 years ago

Hi Volkan, Can you try using the latest pre-release of GangSTR? We recently fixed a bug that caused core-dump in Ubuntu 20.04 due to a change in compiler optimization. https://github.com/gymreklab/GangSTR/releases/tag/v2.4.6 We haven't tried running GangSTR on a Fedora system, but our lab uses a CentOS server (which I believe is a derivative of Fedora, correct me if I'm wrong, as I'm not super familiar with Linux distros). So I assume there shouldn't be any major compatibility issues. Let me know if the latest pre-release didn't work.

mvcakir commented 3 years ago

Dear Nima,

Thanks for the quick response and for the help. Last release seems to solve the issue also for the Fedora.

Volkan