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morispi / CONSENT

Scalable long read self-correction and assembly polishing with multiple sequence alignment
https://doi.org/10.1038/s41598-020-80757-5
GNU Affero General Public License v3.0
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Error in conda version #33

Open SwiftSeal opened 2 years ago

SwiftSeal commented 2 years ago

I tried using the conda installation of CONSENT but it was failing to polish the example reads:

CONSENT-polish --contigs example/rawAssembly.fasta --reads example/reads.fasta --out example/polishedAssembly.fasta
[Tue 18 Jan 14:15:53 GMT 2022] Aligning the long reads to the contigs (minimap2)
[Tue 18 Jan 14:15:57 GMT 2022] Processing the overlaps
/mnt/shared/scratch/apps/conda/envs/CONSENT/bin/CONSENT-polish: line 193: reformatPAF: command not found

I looked at the conda bin and noticed that 'reformatPAF' was actually 'CONSENT-reformatPAF'. Renaming it to this on line 193 of CONSENT-polish fixed this error.

(Not sure if this is the right place to report errors in the conda version!)

richardstoeckl commented 1 year ago

This problem still exists.

pmenzel commented 1 year ago

This should probably fixed in the patches done in the bioconda recipe here: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/consent/CONSENT-polish.patch