MissingOutputException in rule run_phables in file ../phables-1.0.0/lib/python3.10/site-packages/phables/workflow/rules/phables.smk

[minhtrung1997]

Describe the bug A clear and concise description of what the bug is. I run: phables run --input '/home/ktest/share/test/WGS/BACSHORT/Phase_1/tv_230703_testskip_bacshort/Assembly/unicycler/2205SEQ004__UV4_3/2205SEQ004__UV4_3_graph.gfa' --reads reads/ --output check_phage --threads 30

It produces:

2023-07-10 23:39:16,471 - INFO - Total number of genomes resolved: 0
2023-07-10 23:39:16,471 - INFO - No genomes were resolved.
2023-07-10 23:39:16,476 - INFO - Elapsed time: 2.5452001094818115 seconds
2023-07-10 23:39:16,476 - INFO - Thank you for using Phables!
Waiting at most 5 seconds for missing files.
MissingOutputException in rule run_phables in file /home/ktest/pipeline_env/software/environment/Trung_conda/phables-1.0.0/lib/python3.10/site-packages/phables/workflow/rules/phables.smk, line 1:
Job 9  completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
check_phage/resolved_paths.fasta
check_phage/resolved_phages
Removing output files of failed job run_phables since they might be corrupted:
check_phage/resolved_genome_info.txt, check_phage/resolved_edges.fasta, check_phage/resolved_component_info.txt, check_phage/component_phrogs.txt
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Log file Add any other context about the problem here. snamake.log

[Vini2]

Hi @minhtrung1997,

Thanks for posting this issue! Looks like there were no phage genomes identified. I will add a fix so that phables will finish successfully even though there were no genomes identified. The new version of phables should be able to detect more genomes, which will be released soon.

Thanks!

[Vini2]

Hello! Letting you know that I've added a new version of Phables to bioconda.