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bhattlab / lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
MIT License
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circularization error #23

Open saras224 opened 3 years ago

saras224 commented 3 years ago

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

saras224 commented 3 years ago

@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

xmeng commented 2 years ago

I encountered the exact same errors. Any clues?

Thanks, xmeng