Mash 2.1 error in nullarbor v2.0.20181010: option p cannot be used with r

[ropolomx]

Hi Torsten, Thanks for the amazing work with nullarbor! I am very excited to work with it. I am trying to run nullarbor using shovill as the assembler. However, I find that there is an error that I suspect is connected to using mash 2.1. When I try using shovill in a different conda environment that has mash 2.0, shovill runs successfully However, since nullarbor needs mash version 2.1, I can't use version 2.0.

The error message is below. I can show you the complete log if necessary.

[shovill] Read stats: min_len = 30
[shovill] Read stats: avg_len = 141
[shovill] Read stats: total_bp = 86125082
[shovill] Read stats: max_len = 151
[shovill] Estimating genome size with 'mash'
[shovill] Running: mash sketch -o /tmp/X1xwU4nQ88/sketch -p 11 -k 32 -m 3 -r \/home\/jinl\/Long\/AMR\/Sequences_for_uploads\/Mh_test_shovill\/105N\/R1\.fq\.gz 2>&1 | sed 's/^/[mash] /' | tee -a shovill.log
[mash] ERROR: The option p cannot be used with r.
[shovill] Could not determine genome size from ''
Makefile:130: recipe for target '105N/contigs.fa' failed

[esteinig]

Hi @ropolomx - I ran into this issue as well. Torsten opened an issue here. I fixed this temporarily by reverting back to the Mash 2.0, for instance in conda with force uninstall (to prevent removing Shovill dependency) and reinstall with correct version:

conda remove -n your_env mash
conda install -c conda-forge -c bioconda mash=2.0

[tseemann]

This was fixed in shovill here: https://github.com/tseemann/shovill/commit/3fe8e193a8c1f1bf9a1cfc1a79c86b1bda5969e1

I tagged the 1.0.4 release: https://github.com/tseemann/shovill/archive/v1.0.4.tar.gz

The brew package is up to date, but someone will need to update the conda one.

Thank you @esteinig for the conda solution!

[ropolomx]

Thanks @esteinig and @tseemann for your comments! I installed the 1.0.4 release of shovill for the moment. That worked, and that is what I am using to run nullarbor. Unfortunately, downgrading to Mash 2.0 within the conda environment didn't work since nullarbor needs Mash 2.1 and stopped the dependency check after it found Mash 2.0. Thanks again for your suggestions!

[esteinig]

Ah, apologies @ropolomx tested it on Shovill directly not Nullarbor :) Glad to see the fix @tseemann, fast as always!

[druvus]

Shovill is now updated also in bioconda.

[ropolomx]

Thanks @esteinig for the conda solution! It did work for the environment where I was working with shovill and not nullarbor. Thanks @druvus for letting us know! Very much appreciated!!