Hi,
I am getting the following message when running HISAT2. Do you know what the problem might be?
Fatal error: Exit code 1 () Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or -T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required) -@ INT Set number of sorting and compression threads [1]
Legacy usage: samtools sort [options...] <in.bam> <out.prefix> Options: -f Use <out.prefix> as full final filename rather than prefix -o Write final output to stdout rather than <out.prefix>.bam -l,m,n,@ Similar to corresponding options above Error while flushing and closing output libc++abi.dylib: terminating with uncaught exception of type int (ERR): hisat2-align died with signal 6 (ABRT)
Are you getting this on Galaxy? This makes sense as an error on the command line, but less so on Galaxy where the version of samtools should be < 1.3.