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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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mpileup fail to execute bin/sh #514

Open Axze-rgb opened 10 months ago

Axze-rgb commented 10 months ago

Hello, here is my command, using the last stable binary release. I am in Ubuntu 22.04

sambamba mpileup --tmpdir=sambamba_bin GC114716.recal.bam --samtools mpileup -t 20 Chrom_3:1000-1001

I get this error message

sambamba-pileup: Failed to execute '/gnu/store/rib9g2ig1xf3kclyl076w28parmncg4k-bash-minimal-5.1.16/bin/sh' (No such file or directory)
std.exception.ErrnoException@std/stdio.d(639): Cannot open file `sambamba_bin/sambamba-pid290934-ukbx/18.bed' in mode `w' (No such file or directory)

I tried with or without specifying a tmpdir. I don't understand the error message. Any idea of what is happening?

Thanks