localrule verkko

[nickgladman]

Hello,

Thanks for the great resource! I was running verkko v1.4.1 with the following commands.

verkko \
-d asm_seed_max_length10000\
--local-memory 96 \
--seed-max-length 100000 \
--hifi hifi_reads.fastq.gz.fastq.gz \
--nano ont_merged.fastq.gz

It seemed like it ran fine, but the end of the log file gave this notification and I wanted to make sure nothing major was wrong. I saw that v2.0 is live so I'll re-run the assembly, but I appreciate any insight.

Finished job 19.
276 of 277 steps (99.6%) done
Select jobs to execute...

[Sat Dec  2 07:03:08 2023]
localrule verkko:
    input: 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.gfa, emptyfile, 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, emptyfile, emptyfile, 2-processGraph/unitig-unrolled-hifi-resolved.hifi-coverage.csv, 2-processGraph/unitig-unrolled-hifi-resolved.ont-coverage.csv, 4-processONT/unitig-unrolled-ont-resolved.hifi-coverage.csv, 4-processONT/unitig-unrolled-ont-resolved.ont-coverage.csv, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.hifi-coverage.csv, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.ont-coverage.csv
    output: assembly.homopolymer-compressed.gfa, assembly.homopolymer-compressed.noseq.gfa, assembly.homopolymer-compressed.layout, assembly.hifi-coverage.csv, assembly.ont-coverage.csv, assembly.fasta, assembly.scfmap
    jobid: 0
    reason: Missing output files: assembly.homopolymer-compressed.layout, assembly.fasta, assembly.homopolymer-compressed.gfa, assembly.scfmap, assembly.ont-coverage.csv, assembly.hifi-coverage.csv, assembly.homopolymer-compressed.noseq.gfa; Input files updated by another job: 7-consensus/unitig-popped.fasta, 7-consensus/unitig-popped.unassigned.fasta, 7-consensus/unitig-popped.haplotype2.fasta, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.ont-coverage.csv, 6-layoutContigs/unitig-popped.layout.scfmap, emptyfile, 2-processGraph/unitig-unrolled-hifi-resolved.hifi-coverage.csv, 2-processGraph/unitig-unrolled-hifi-resolved.ont-coverage.csv, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.hifi-coverage.csv, 6-layoutContigs/unitig-popped.layout, 4-processONT/unitig-unrolled-ont-resolved.ont-coverage.csv, 7-consensus/unitig-popped.haplotype1.fasta, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.gfa, 4-processONT/unitig-unrolled-ont-resolved.hifi-coverage.csv
    resources: tmpdir=/tmp/6903245.1.comp.q

Reading graph from stdin
[Sat Dec  2 07:03:19 2023]
Finished job 0.
277 of 277 steps (100%) done
Complete log: .snakemake/log/2023-12-01T092225.943301.snakemake.log

[brianwalenz]

Looks good! If you've got a big pile of assembly.* files in the main output directory (all the files listed in 'output'), it's done!

The log is saying that rule 'verkko' needs to run because of 'reason': that the output files don't exist. All this rule does is copy files to the proper output names.

[skoren]

Idle