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seg fault for reheader -o #2311

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Ahuiting opened this issue Oct 30, 2024 · 3 comments
Open

seg fault for reheader -o #2311

Ahuiting opened this issue Oct 30, 2024 · 3 comments

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@Ahuiting
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Hello, I want to change the sample name of .g.vcf.gz files, and it threw seg fault.
bcftools reheader -s <(echo "old_name" "new_name") -o folder/output.g,vcf.gz input.g.vcf.gz
But i found the problem is permission denied by 'folder', i also tested it with no existing folder path, it threw seg fault too.

The bcftools version is :
bcftools 1.21
Using htslib 1.21
Copyright (C) 2024 Genome Research Ltd.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

@pd3
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pd3 commented Oct 31, 2024

I am unable to reproduce the problem. Can you provide a small test case? This works just fine for me

$ mkdir xx
$ chmod -rxw xx
$ bcftools reheader -s <(echo old_name new_name) rmme.vcf -o xx/rmme.vcf
xx/rmme.vcf: Permission denied

@Ahuiting
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Ahuiting commented Nov 5, 2024

I am unable to reproduce the problem. Can you provide a small test case? This works just fine for me

$ mkdir xx
$ chmod -rxw xx
$ bcftools reheader -s <(echo old_name new_name) rmme.vcf -o xx/rmme.vcf
xx/rmme.vcf: Permission denied

Thanks for replying, I tried same commands, but i still get seg fault.

mkdir test
bcftools reheader -s <(echo 'old' 'new')  -o test/new_name.g.vcf.gz test.g.vcf.gz   

this works for me, but after i changed permission, it threw Seg fault.

chmod -rxw test                                                                                                                       
bcftools reheader -s <(echo 'old' 'new')  -o test/new_name.g.vcf.gz test.g.vcf.gz
Segmentation fault 

I also tried same commands on my own laptop.

bcftools reheader -s <(echo 'old' 'new')  test.g.vcf.gz -o test/new_name.g.vcf.gz 
zsh: segmentation fault  bcftools reheader -s <(echo 'old' 'new') test.g.vcf.gz -o 

@pd3
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pd3 commented Nov 6, 2024

It seems the problem is not with permissions but with something else. Any chance you could share a small test case to reproduce the problem?

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