Comments (4)
Hi @slzarate ,
I reached out to our VG collaborators. I'll keep an eye on this to make sure you can get some answers.
(I don't know the answer myself)
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If sra.fq.paths
is a list of input files, it should be entered as @sra.fq.paths
. KMC does not attempt to identify the input type. If not specified otherwise, it seems to assume that the input is (plain or gzipped) fastq.
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@pichuan @jltsiren Thank you! That did it.
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You need to prefix your paths file with @
. So try
time ./kmc -k29 -okff -t8 @sra.fq.paths ./sra.fq $TMPDIR
(edit: oops, sorry for repeated post -- somehow didn't notice reply above)
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