When I try to produce the consensus marker files:
Command:
sample2markers.py -i SRS013951.sam.bz2 -o consensus_markers -n 40
Error:
Sun Dec 20 19:01:59 2020: Start samples to markers execution
Sun Dec 20 19:01:59 2020: Decompressing samples…
Sun Dec 20 19:02:01 2020: Done.
Sun Dec 20 19:02:01 2020: Converting samples to BAM format…
[samopen] SAM header is present: 1132380 sequences.
Sun Dec 20 19:02:09 2020: Done.
Sun Dec 20 19:02:09 2020: Sorting BAM samples…
[e] Parallel execution fails: [Errno 2] No such file or directory: ‘consensus_markers/tmp/SRS013951.sorted.bam’
Sun Dec 20 19:02:14 2020: Stop StrainPhlAn 3.0 execution.
I’m sure that the SRS013951.sam.bz2 is right (down load from your wedsite).
I don’t know why the samtools don’t when the python script use it.