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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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aborted on example data #36

Open dinovski opened 1 year ago

dinovski commented 1 year ago

Hi,

Installation of CONSENT and dependencies completed without any warnings or issues on a GNU/Linux VM: Linux ip-172-26-3-204 5.10.0-19-cloud-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 GNU/Linux

but the example failed with the following error:

./CONSENT-correct --in example/reads.fasta --out example/correctedReads.fasta --type PB [Fri Jan 13 16:19:16 UTC 2023] Overlapping the long reads (minimap2) [Fri Jan 13 16:19:25 UTC 2023] Correcting the long reads free(): invalid next size (normal) ./CONSENT-correct: line 202: 321161 Aborted $LRSCf/bin/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"

Any help would be appreciated!

rmormando commented 1 year ago

I get the same error message when I try to run it as well...did anyone find a solution?