emjbishop
commented
5 months ago 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
When it comes to test files, it is running fine, but with my own data .bam file it is giving me empty fastq files at partial typing and I don't know why it is so? My email address is mahlaranjeet@gmail.com; if you can suggest me the cause, please get back to me, I can share my bam file with you.