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Error during correction #37

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desmodus1984 opened this issue Sep 25, 2023 · 0 comments
Open

Error during correction #37

desmodus1984 opened this issue Sep 25, 2023 · 0 comments

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@desmodus1984
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Hi,
Hope you are doing great.
I did a quick Nanopore run, and I got some data that I would like to correct.
I am running CONSENT and it is failing after changing different parameters, like -j or -k.

Error:
"
CONSENT-correct --type ONT --in Bc.04.fasta --out Bc.04.corr.fasta
[Mon Sep 25 13:31:55 EDT 2023] Overlapping the long reads (minimap2)
[Mon Sep 25 13:32:19 EDT 2023] Correcting the long reads
/home/juaguila/.conda/envs/consent/bin/CONSENT-correct: line 202: 106441 Illegal instruction 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"
"

My dataset stats are: min: 43, max: 134,709, average: 6.642, and about 35,464 sequences, size: 238M.

Any reason why CONSENT is failing?
I base-called it with Guppy, then merged the gz files, and then converted the fastq with seqkit to fasta.

Thanks;

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