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a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.
https://a-ludi.github.io/dentist/
MIT License
47 stars 6 forks source link

Rerun after stop due to time limit #41

Closed aureliendejode closed 1 year ago

aureliendejode commented 1 year ago

Hello,

I am ran the snakemake pipeline from on a slurm cluster in a single job using sbatch. It stopped due to time limit and now when I try to rerun it, it just list a bunch of job and stops again without clear explanation. Any idea what is going on ?

Here is my script

snakemake --configfile=snakemake.yml --use-conda --cores=all --rerun-incomplete --unlock snakemake --configfile=snakemake.yml --use-conda --cores=all --rerun-incomplete

a-ludi commented 1 year ago

AFAIK there is no need for --rerun-incomplete. Actually, I think that might be the culprit.

Please adjust the cluster config to increase time limits.

aureliendejode commented 1 year ago

Hi, So I removed --rerun-incomplete and started from scratch with more resources and it ran well. I am wondering now at what output should I look to know how many gaps were closed and how they were validated ? Is it all in the report.json ?

Best

a-ludi commented 1 year ago

Glad it worked!

You will want to look at the *.closed-gaps.bed first. It describes the locations of closed gaps in the result FASTA – one line per closed gap. The *.agp provide a little more information how the assembly is structured but is much harder to read.

The report.json provides details on the results of the automatic validation. It may be useful if you have gap a that was not closed and are wondering why. But its not the only place to - look for, see #33.

a-ludi commented 1 year ago

The main reason for this issue is fixed so I will close this issue. Please feel free to open a new one if you need further help or guidance.