Always Segmentation fault when running frequency

[xiekunwhy]

Hi,

when running grenedalf frequency (v0.6.3 from conda), grenedalf always Segmentation fault. fst and diversity finish normally.

#!/bin/bash
/public2/home/sl_qybio/sl_qybio/miniforge3/envs/grenedalf/bin/grenedalf frequency --write-sample-counts --sam-path bam --sam-min-map-qual 5 --reference-genome-fasta mpe.fa --out-dir freq --allow-file-overwriting --threads 40

/opt/gridview/slurm/spool/slurmd_c074/job4440997/slurm_script: line 2: 345289 Segmentation fault     /public2/home/sl_qybio/sl_qybio/miniforge3/envs/grenedalf/bin/grenedalf frequency --write-sample-counts --sam-path bam --sam-min-map-qual 5 --reference-genome-fasta mpe.fa --out-dir freq --allow-file-overwriting --threads 40

Best,
Kun

[lczech]

Hi Kun,

I just tested your exact command with some bam files, and it worked for me. So in order to reproduce and investigate, I will need the files (bam and ref genome) that you are using. Could you please share them?

So long
Lucas

[xiekunwhy]

Can you use BaiDu Netdisk (https://pan.baidu.com) ? The bam files are very large (23G in total) and I can not attach here.

[lczech]

In that case, could you subset them to a smaller size (and make sure that the issue still occurs)? If the issue only happens with those big files, hm, yes, we could try BaiDu.