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bhattlab / lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

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circularization error

saras224 opened this issue · comments

commented

Hi @elimoss
After 11 days of assembly, process stopped while circularization of genomes.
error:
Activating singularity image /lustre/rsharma/.snakemake/singularity/f075a3ce7bc1893be5302161e5e7807a.simg
Waiting at most 30 seconds for missing files.
MissingOutputException in line 574 of /home/rsharma/lathe/Snakefile:
Job Missing files after 30 seconds:
W1/3.circularization/1.candidate_genomes
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Job id: 25 completed successfully, but some output files are missing. 25
Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
Complete log: /lustre/rsharma/.snakemake/log/2021-08-12T150046.064606.snakemake.log
{'W1': ['/home/rsharma/WWK_forward_paired.fastq', '/home/rsharma/WWK_reverse_paired.fastq']}
Checking for updates or modifications to workflow
WARNING: Differences to latest version detected. Please reset changes and/or pull repo.

Please help me figure out what is the problem.

Thanks
Saraswati

commented

@dgmaghini
Hi
would this problem be solved if I increase the latency wait?
I checked the snakmake log it says there is an error in line 574 :
Activating singularity image /lustre/rsharma/.snakemake/singularity/f075a3ce7bc1893be5302161e5e7807a.simg
Waiting at most 30 seconds for missing files.
MissingOutputException in line 574 of /home/rsharma/lathe/Snakefile:
Job Missing files after 30 seconds:
W1/3.circularization/1.candidate_genomes
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Job id: 25 completed successfully, but some output files are missing. 25
Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
Complete log: /lustre/rsharma/.snakemake/log/2021-08-12T150046.064606.snakemake.log
{'W1': ['/home/rsharma/WWK_forward_paired.fastq', '/home/rsharma/WWK_reverse_paired.fastq']}
Checking for updates or modifications to workflow
WARNING: Differences to latest version detected. Please reset changes and/or pull repo.

Also Do I have to start the assembly pipeline from beginning or it can be started from circularization?

Thanks
Saraswati

commented

I encountered the exact same errors. Any clues?

Thanks,
xmeng