Comments (1)
I had the same issue with bam files sorted and indexed using samtools in my base conda environment. Turns out the samtools version installed with arcasHLA via conda doesn't work on my machine. You can test this for yourself by trying to run $ samtools
within your arcas-hla environment.
To fix this, I downloaded and installed the tar.gz of the samtools version that works in my base environment (identified the version via conda list
):
(arcas-hla) [04/02/24 13:11:38] emmabishop@bioinfo:~/Downloads$ wget https://anaconda.org/bioconda/samtools/1.6/download/linux-64/samtools-1.6-hb116620_7.tar.bz2
(arcas-hla) [04/02/24 13:13:14] emmabishop@bioinfo:~/Downloads$ conda install samtools-1.6-hb116620_7.tar.bz2
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