The --paths option can re-run the pipeline when initial asm or input file timestamps are updated

[skoren]

Since snakemake relies on timestamps to decide what needs to re-run, any changes to the initial assembly (the --assembly option) for the --paths pipeline can cause verkko to restart from scratch, generating an invalid results and usually crashing in the process.

We should add something to check that only the intended steps are being run before launching snakemake to avoid this issue for users.

[likai888]

Thank you for your timely supplement. I may have encountered a similar problem, but I'm not sure if it is: I got "[Errno 122] Disk quota exceeded" when running verkko --snakeopts "-- touch". I modified timestamps of the initial assembly.
So, how to address this trouble.

command :

verkko
--snakeopts '--touch'
-d verkko_final_asm
--slurm
--hifi-coverage 35
--hifi ./PacBio_HiFi/hifi_reads.fastq.gz
--nano ./ONT///.fastq.gz
--paths ./verkko_v2.2/manual.paths.gaf
--assembly ./verkko_v2.2/

slurm out

Launching release v2.2.1
Using snakemake 7.32.4.
Using profile /miniconda3/envs/py3/lib/verkko/profiles for setting default command line arguments.
OSError in file /miniconda3/envs/py3/lib/verkko/Snakefile, line 215:
[Errno 122] Disk quota exceeded
File "/miniconda3/envs/py3/lib/verkko/Snakefile", line 215, in
File "/miniconda3/envs/py3/lib/python3.8/tempfile.py", line 515, in close
File "/miniconda3/envs/py3/lib/python3.8/tempfile.py", line 449, in close

[skoren]

No your error looks like you're out of disk, not sure if that's on your main location where you're running verkko or where snakemake writes some logs (see #124) but either way until you free up space you can't test if the run will be correct.

[likai888]

Thank you Sergey,
Yes, it was out of disk. The snakemake need some space from out of working directory. we fixed it, thanks.

best regard,
Kai

[likai888]

Happy new year, Sergey,
I utilized removeRDNA.sh and manually edited the rukki.paths.gaf file. When I attempted to use the --paths option, it seemed that verkko restarted from the beginning. Despite using --snakeopts '--touch', it did not alter the timestamps for 0-correction, 6-layoutContigs, and hifi-corrected.fasta.gz. What should I do next? Or is there any way to remedy this situation?
best regard,
Kai

[skoren]

The easiest way would be to erase the old folder where the run started from scratch, make a new folder yourself, symlink the 0- through 5- folders to the old location and then run the --paths again. Try it first with --dry-run to make sure it will do the right thing.