mapping issue #82
Comments
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Actually I found that for some reason the file output/assembly/megahit/coassembly/coassembly.contigs_renamed.fa was 0 bytes. I am running metaphor again, let's see if it fixes it. I'll keep you posted! |
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Unfortunately, it does not work. Metaphor keeps creating an empty assembly/megahit folder (ratherthan empty, actually files are there but are 0 bytes). Can you please help me troubleshooting this Vini? |
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Hi @francesco-ricci, this looks like a problem with the assembly. Could you please post the log of the assembly/megahit process here? Thank you! |
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Hey Vini, thanks for your help. I restarted the full pipeline, if it'll bump into this again I'll post it. Thanks |
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Hi Vini, the problem happened again. This is the assembly report: 2024-07-16 07:51:36 - MEGAHIT v1.2.9 |
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I am running this analysis on a coral dataset using host step removal. This is the only reason why I could think the low number of aligned reads. |
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@francesco-ricci that could very well be the cause. What are the sizes of the input files going into the assembler? |
Hi VIni,
I keep getting this error message:
[Sat Jul 13 01:49:37 2024]
Error in rule concatenate_contigs:
jobid: 56
input: output/assembly/megahit/coassembly/coassembly.contigs_renamed.fa
output: output/mapping/cobinning/cobinning_contigs_catalogue.fna.gz
log: output/logs/mapping/concatenate_contigs/cobinning.log (check log file(s) for error details)
conda-env: /home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/d2f1a35ff4b889a5c9b33f580fd56824_
shell:
MissingOutputException in rule assembly_report in file /home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/workflow/rules/assembly.smk, line 103:
Job 52 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:
output/assembly/assembly_report/avg_length.png (missing locally, parent dir contents: )
output/assembly/assembly_report/max_length.png (missing locally, parent dir contents: )
output/assembly/assembly_report/median_length.png (missing locally, parent dir contents: )
output/assembly/assembly_report/no_bp.png (missing locally, parent dir contents: )
output/assembly/assembly_report/no_contigs.png (missing locally, parent dir contents: )
output/assembly/assembly_report/n50.png (missing locally, parent dir contents: )
output/assembly/assembly_report/assembly_report.tsv (missing locally, parent dir contents: )
Removing output files of failed job concatenate_contigs since they might be corrupted:
output/mapping/cobinning/cobinning_contigs_catalogue.fna.gz
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-07-10T173408.447387.snakemake.log
WorkflowError:
At least one job did not complete successfully.
Traceback (most recent call last):
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/bin/metaphor", line 10, in
sys.exit(main())
^^^^^^
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/cli.py", line 278, in main
args.func(args)
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/execute.py", line 109, in main
retcode = run_cmd(cmd)
^^^^^^^^^^^^
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/utils.py", line 92, in run_cmd
retcode = check_call(cmd.split())
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['snakemake', '--snakefile', '/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/workflow/Snakefile', '--configfile', 'metaphor_set>
This is what the output of logs/mapping/cobinning.log looks like:
Traceback (most recent call last):
File "/home/fricci/rp24/fra/software/miniconda3/envs/checkm/bin/concatenate.py", line 42, in
vamb.vambtools.concatenate_fasta(filehandle, args.inpaths, minlength=args.minlength,
File "/home/fricci/rp24/fra/software/miniconda3/envs/checkm/lib/python3.10/site-packages/vamb/vambtools.py", line 555, in concatenate_fasta
for entry in entries:
File "/home/fricci/rp24/fra/software/miniconda3/envs/checkm/lib/python3.10/site-packages/vamb/vambtools.py", line 272, in byte_iterfasta
raise ValueError('Empty or outcommented file')
ValueError: Empty or outcommented file
Can you help me with this?
Thanks
Francesco
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