Skip to content

aborted on example data #36

@dinovski

Description

@dinovski

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!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions