35 days and going - is it normal to take this long?

[katiecdillon]

Hello,

This is my first time running CONSENT. My input file is raw, ONT genome reads from the tick D. reticulatus (27,098,808 reads). Below is my submission script. The script has been running for 35+ days so far. Do you think this is normal?

#!/bin/bash #SBATCH --job-name=CONSENT #SBATCH --partition=iob_p #SBATCH --ntasks=1 #SBATCH --cpus-per-task=16 #SBATCH --mem=500gb #SBATCH --export=NONE #SBATCH --time=30- #SBATCH --output=%x_%j.out #SBATCH --error=%x_%j.err #SBATCH [email protected] #SBATCH --mail-type=BEGIN,END,FAIL

ml CMake/3.26.3-GCCcore-12.3.0 minimap2/2.26-GCCcore-12.2.0

raw_reads='/scratch/kcd88651/ticks/Dermacentor_Reticulatus/raw_reads/4_R9R10_G638_combo.fastq'

git clone --recursive https://github.com/morispi/CONSENT

cd CONSENT ./install.sh

cd CONSENT ./CONSENT-correct --in $raw_reads --out Dr_4_R9R10_G638_combo_CONSENTc.fasta --type ONT

[katiecdillon]

Update:

CONSENT finished today but threw an error after running for nearly 50 days and produced an empty FASTA file:

terminate called after throwing an instance of 'std::invalid_argument' what(): stoi ./CONSENT-correct: line 202: 1971601 Aborted (core dumped) $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"