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vpc-ccg / haslr

A fast tool for hybrid genome assembly of long and short reads
GNU General Public License v3.0
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ERROR: "haslr_assemble" returned non-zero exit status #35

Open mictadlo opened 2 years ago

mictadlo commented 2 years ago

Hi,

$ haslr.py --contig megahit-final.contigs.fa --cov-lr 0 -t 8 -o results -g 2.7g -l N_sylvestris_UL.fastq -x nanopore

checking /work/waterhouse_team/apps/haslr/bin/haslr_assemble: ok
checking /work/waterhouse_team/apps/haslr/bin/minia_nooverlap: ok
checking /work/waterhouse_team/apps/haslr/bin/fastutils: ok
checking /work/waterhouse_team/apps/haslr/bin/minia: ok
checking /work/waterhouse_team/apps/haslr/bin/minimap2: ok
number of threads: 8
output directory: /lustre/scratch/waterhouse_team/Nsylvestris/megahit/haslr/results
[24-Feb-2022 06:55:55] renaming long reads and storing in /lustre/scratch/waterhouse_team/Nsylvestris/megahit/haslr/results/lrall.fasta... done
[24-Feb-2022 06:58:13] removing overlaps in short read assembly... done
[24-Feb-2022 06:58:26] removing short sequences in short read assembly... done
[24-Feb-2022 06:58:37] aligning long reads to short read assembly using minimap2... done
[24-Feb-2022 09:39:49] assembling long reads using HASLR... failed
ERROR: "haslr_assemble" returned non-zero exit status

What did I miss?

Thank you in advance,

Michal