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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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"xargs: illegal option -- -" leading to "No files found with .faa suffix in input directory" #110

Closed SvenTobias-Hunefeldt closed 4 years ago

SvenTobias-Hunefeldt commented 4 years ago

Hi!

I've been trying to use this tool to annotate a prodigal output, and get the % of kegg module completeness.

Running this: enrichm annotate --protein_directory Samples --ko --threads 2 --force

Leads to this:

[2020-08-06 10:54:32 AM] INFO: Command: /usr/local/bin/enrichm annotate --protein_directory Samples --ko --threads 2 --force --verbosity 5
[2020-08-06 10:54:32 AM] INFO: Running the annotate pipeline
[2020-08-06 10:54:32 AM] INFO: Running pipeline: annotate
[2020-08-06 10:54:32 AM] INFO: Setting up for genome annotation
[2020-08-06 10:54:32 AM] INFO: Using provided proteins
[2020-08-06 10:54:32 AM] INFO: Preparing genomes for annotation
[2020-08-06 10:54:32 AM] DEBUG: xargs --arg-file=/dev/stdin ln -s --target-directory=2020-08-06_10-54-enrichm_annotate_output/genome_proteins
xargs: illegal option -- -
usage: xargs [-0opt] [-E eofstr] [-I replstr [-R replacements]] [-J replstr]
             [-L number] [-n number [-x]] [-P maxprocs] [-s size]
             [utility [argument ...]]
[2020-08-06 10:54:32 AM] ERROR: No files found with .faa suffix in input directory
[2020-08-06 10:54:32 AM] INFO: Finished running EnrichM

It seems to be the annotate.py script that's running into issues recognising files within the supplied directory. Specifically I think this is the line that's failing:

cmd = "xargs --arg-file=/dev/stdin ln -s --target-directory=%s" % genome_directory I've already made changes as suggested with Issue number #94, but it didn't seem to help.

These are the package versions I'm using on a Mac: enrichM 0.5.0 hmmer 3.3.1 diamond 0.9.36 ( I can't seem to install version 0.9.22 as the installation instructions recommend) prodigal 2.6.2 parallel 0200722 MMseqs2 11-e1a1c_1 R 4.0.2_1 mcl 14-137