Snakemake error while running MetaCompass (unrecognized arguments: -T)

[ciemanek]

When I try to run MetaCompass on my single-end reads, I get the following error:

snakemake: error: unrecognized arguments: -T

I go for my own reference genome and the command I use to run MetaCompass is as follows:

./MetaCompass/go_metacompass.py -U sample.fastq -r reference.fasta -o workdir/assembly/metacompass

[vcepeda]

were you able to run the readme examples successfully? The -T option is run internally by go_metacompass.py. What is your version of snakemake?

[ciemanek]

It is the same issue with the examples. i am using snakemake 5.10.0. I tried to find the -T parameter in snakemake documentation and the closest I found was -t (-touch) - was meant to be the one?

[vcepeda]

the -T parameter prints timestamps. I added the new script "go_metacompass2.py" that doesn't use that option for testing. Please let me know if it works for you.

[ciemanek]

thank you! it resolved the -T parameter issue, however I get the error abut buildcontig being missing:

bash: (...)/MetaCompass/bin/buildcontig: No such file or directory

[vcepeda]

That means that you didn't run the install.sh script that compiles the buildcontig assembler. Please run it to generate all the required components.