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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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lr0x.fasta... [ERROR] option -d/--depth is required #32

Closed mictadlo closed 2 years ago

mictadlo commented 2 years ago

Hi, I have got lr0x.fasta... [ERROR] option -d/--depth is required

conda activate haslr
haslr.py --minia-kmer $k --cov-lr 0 -t 8 -o results -g 3.2g -l ../allPacBio.fasta -x pacbio -s ../1740D-43-03_S0_L001_R1.fastq.gz ../1740D-43-03_S0_L001_R2.fastq.gz

checking /work/waterhouse_team/miniconda2/envs/haslr/bin/haslr_assemble: ok
checking /work/waterhouse_team/miniconda2/envs/haslr/bin/minia_nooverlap: ok
checking /work/waterhouse_team/miniconda2/envs/haslr/bin/fastutils: ok
checking /work/waterhouse_team/miniconda2/envs/haslr/bin/minia: ok
checking /work/waterhouse_team/miniconda2/envs/haslr/bin/minimap2: ok
number of threads: 8
output directory: /lustre/scratch/waterhouse_team/NWA/haslr-ks/95/results
subsampling 0x long reads to /lustre/scratch/waterhouse_team/NWA/haslr-ks/95/results/lr0x.fasta... [ERROR] option -d/--depth is required

done
assembling short reads using Minia... done
removing overlaps in short read assembly... done
removing short sequences in short read assembly... done
aligning long reads to short read assembly using minimap2... done
assembling long reads using HASLR... done

What did I miss?

Thank you in advance,

Michal

mictadlo commented 2 years ago

Sorry, I ran bioconda version which did not support --cov-lr 0