Strainphlan consensus markers

Microbial community profiling StrainPhlAn
1

Hi there, I am using Strainphlan 4, and am able to make Sam files.
However, when I try to make consensus markers I get the following error:

[Error] Parallel execution fails: Compressed file ended before the end-of-stream marker was reachedWed Sep 11 23:57:51 2024: Stop StrainPhlAn execution.

This is my code:

mkdir consensus_markers4
sample2markers.py -i sams2/sams/*.sam.bz2 -o consensus_markers4 --nproc 4

Thank you!

2

Hi, this looks like a problem with the sam.bz2 file (incomplete file). Probably there was an error while running metaphlan to produce them. Can you re-run metaphlan and check the output that it doesn’t throw an error?