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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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Problem - reformatPAF #39

Open desmodus1984 opened 1 month ago

desmodus1984 commented 1 month ago

Hi,

I am trying to correct a mitochondrial genome assembly, I thought it would be simple and straightforward, and I got an error: I created a new conda environment, no issue during installation, but I got an error:

CONSENT-polish --contigs Ju760.3x_final.fa --reads ../Ju760.3x.q20.rename.fq --out Ju760.3x_polish.fa [Thu Jul 18 05:56:02 PM EDT 2024] Aligning the long reads to the contigs (minimap2) [Thu Jul 18 05:56:03 PM EDT 2024] Processing the overlaps /home/juaguila/miniconda3/envs/consent/bin/CONSENT-polish: line 193: reformatPAF: command not found

Could you tell why this happened with a fresh installation? Thanks;

desmodus1984 commented 1 month ago

Also, I tried to correct my mtDNA reads, which make just 2.7Mb, and I ran this code: CONSENT-correct --in Ju760.3x.q20.fq --out Ju760.3x.corr.fasta --type ONT -j 12 And I got an error again: [Thu Jul 18 06:00:17 PM EDT 2024] Overlapping the long reads (minimap2) [Thu Jul 18 06:00:18 PM EDT 2024] Correcting the long reads /home/juaguila/miniconda3/envs/consent/bin/CONSENT-correct: line 202: 2699400 Segmentation fault (core dumped) CONSENT-correction -a $tmpdir/"$alignments" -s "$minSupport" -S "$maxSupport" -l "$windowSize" -k "$merSize" -c "$commonKMers" -A "$minAnchors" -f "$solid" -m "$windowOverlap" -j "$nproc" -r "$reads" -M "$maxMSA" -p "$LRSCf" >> "$out"

Thanks;