search

marbl / verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
290 stars 29 forks source link

ERROR in combineConsensus #267

Closed KANGYUlab closed 2 months ago

KANGYUlab commented 3 months ago

Hi, when i run verkko : verkko -d ont_herro-nocorr --hifi herro/porechopped.fa.gz --nano ont.fa.gz --hap-kmers M.hapmer.meryl P.hapmer.meryl trio --threads 64 --local --local-memory 200 --no-correction

It stopped at 7-consensus combineConsensus, reported: ERROR: contig M.hapmer-0004259 is empty. ERROR: piece piece000019 missing from gapped contig P.hapmer-0004316.

Did the parameter setting "--no-correction" cause the problem?

Thank you so much.

Dmitry-Antipov commented 3 months ago

Hi, It should not be related. Which version of verkko do you use? There was an issue in verkko2.0 with this symptoms, but it should be fixed in verkko2.1

KANGYUlab commented 3 months ago

Yes, it run in verkko2.0, I will try again. Thank you.

Dmitry-Antipov commented 2 months ago

Please reopen this issue if you see the same in 2.1

gdroc commented 2 months ago

Hi, I used the last version (2.1). When I run verkko (Hic mode) with verkko --cleanup --threads 32 -d results/C45_410/assembly/verkko/ --hifi data/C45_410.fastq.gz --hic1 data/DTG_OmniC_974/DTG_OmniC_974_CKDL240006666-1A_22JKVWLT3_L8_R1.fastq.gz --hic2 data/DTG_OmniC_974/DTG_OmniC_974_CKDL240006666-1A_22JKVWLT3_L8_R2.fastq.gz --slurm --snakeopts " --cores 200 --cluster './slurm-sge-submit.sh {threads} {resources.mem_gb} {resources.time_h} {rulename} {resources.job_id} -p agap_long'"

I have got an error (8-hicPipeline/final_contigs/7-consensus/combineConsensus.err) ERROR: contig contig-0000782 is empty.

Snakemake process was at the end [Mon Jul 15 01:10:14 2024] localrule cnspath: input: 6-layoutContigs/unitig-popped.layout, 6-layoutContigs/unitig-popped.layout.scfmap, 7-consensus/unitig-popped.fasta, 7-consensus/unitig-popped.haplotype1.fasta, 7-consensus/unitig-popped.haplotype2.fasta, 7-consensus/unitig-popped.unassigned.fasta output: assembly.homopolymer-compressed.layout, assembly.fasta jobid: 0 reason: Missing output files: assembly.fasta, assembly.homopolymer-compressed.layout; Input files updated by another job: 7-consensus/unitig-popped.fasta, 7-consensus/unitig-popped.haplotype2.fasta, 6-layoutContigs/unitig-popped.layout.scfmap, 7-consensus/unitig-popped.haplotype1.fasta, 7-consensus/unitig-popped.unassigned.fasta, 6-layoutContigs/unitig-popped.layout resources: mem_mb=2890, mem_mib=2757, disk_mb=2890, disk_mib=2757, tmpdir=/tmp

[Mon Jul 15 01:10:19 2024] Finished job 0. 500 of 500 steps (100%) done Complete log: .snakemake/log/2024-07-14T062408.640509.snakemake.log

When I look at the final results assembly.haplotype1.fasta and assembly.haplotype2.fasta are empty

What could I try to correct the problem? Regards Gaetan