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rpetit3 / dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
GNU General Public License v3.0
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Execution error with Rasusa v1.0.0 in conda environment #31

Closed nbenzakour closed 6 months ago

nbenzakour commented 6 months ago

Hi,

Thanks for developing Dragonflye—it's been highly useful! I've encountered an issue with Rasusa during installation on a new Ubuntu 22.04 machine using Conda. Dragonflye v1.2.0 seems to pull Rasusa v1.0.0 instead of v0.8.0, leading to a syntax error in the rasusa command.

[...]
[dragonflye] Using rasusa - /opt/conda/envs/dragonflye_1.2.0/bin/rasusa | rasusa 1.0.0
[...]
[dragonflye] Running: rasusa -i READS\.filt\.fq\.gz -c 100 -g 50000 -s 42  2>&1 1> READS.sub.fq | sed 's/^/[rasusa] /' | tee -a dragonflye.log
[rasusa] error: unexpected argument '-i' found
[...]

Correct Rasusa v1.0.0 syntax:

rasusa reads -c 100 -g 50000 -s 42 READS\.filt\.fq\.gz 2>&1 1> READS.sub.fq | sed 's/^/[rasusa] /' | tee -a dragonflye.log

Cheers, Nouri

rpetit3 commented 6 months ago

Hi @nbenzakour

Thank you for reporting this and especially for sharing the new syntax. I've now fixed this, just trying to sort out the CI before submitting a new release.

Cheers, Robert

rpetit3 commented 6 months ago

Ok submitted a new release, https://github.com/rpetit3/dragonflye/releases/tag/v1.2.1

I'll get the bioconda recipe updated as well. Thanks again!