No such file or directory: 'name_sorted_alignment.sam'Īlso throws an error and does not complete but there is no error message.ĪH, Ok, I found the issue. fail to open file name_sorted_alignment.sam HTSeq: Fatal error: Unknown error occured Sort: invalid option - invalid option - '1' data/galaxy/galaxy/database/jobs_directory/000/86/tool_script.sh: line 41: 8799 Exit 1 hisat2 -p $ -l 6 -o '/data/galaxy/galaxy/database/files/000/dataset_131.dat' (ERR): hisat2-align died with signal 13 (PIPE) invalid BAM binary header (this is not a BAM file). Sort: invalid option - invalid option - 'l' Any ideas on this or perhaps a location in the file structure I can look at for more information? Help is greatly appreciated as I have several users waiting for me to fix this issue. It seems all of the mappers are able to do their thing but after the mapping when the tool attempts to sort the output using samtools "sort" that is when the errors are thrown and the jobs cannot be completed. I suspect my issue is something with samtools, however if I look under "Mange Dependencies" all of these tools show the samtools dependency resolved by Conda and actually each mapper uses different versions of samtools. I am having issues with several mapping tools that utilize samtools and I think I have finally identified some commonality between the errors.
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