Snakemake bug #3
Comments
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snakemake/snakemake#823 doesn't provide a good solution. You could try re-running from the start, instead of resuming an old, failed run. It could also be associated with high file latency, but it sounds like you are not using a networked file system. |
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Yes, I re-runed a new analysis and got the same error either using the commands: snakemake --cores all --use-conda Or snakemake --cores all --use-conda --keep-going Do you recommend other command to test your pipeline? Thanks in advanced |
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Thanks for checking. It appears that the BLAST job didn't return any hits, which resulted in a lack of an output file, so the snakemake pipeline run failed. I've added |
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Thank you! Now is running!!! |
I am running the pipeline without problems until I have the next issue about snakemake:
[Sun Sep 25 03:50:46 2022]
rule clusters_blastx_nontarget_format:
input: /home/Documents/coregenomeprimers/last/CoreGenomePrimers/tests/tmp/cabana/CoreGenomePrimers_2359642/blastx_nontarget/hits.txt, /media/backup/DB/accession/nr_accession-geneNames.pkl
output: /home/Documents/coregenomeprimers/last/CoreGenomePrimers/tests/output_pecto/cgp/nontarget/cds_blastx.tsv
log: /home/Documents/coregenomeprimers/last/CoreGenomePrimers/tests/output_pecto/logs/cgp/annotate/blastx_nontarget_format/all.log
jobid: 21
benchmark: /home/Documents/coregenomeprimers/last/CoreGenomePrimers/tests/output_pecto/benchmarks/cgp/annotate/blastx_nontarget_format/all.txt
reason: Missing output files: /home/Documents/coregenomeprimers/last/CoreGenomePrimers/tests/output_pecto/cgp/nontarget/cds_blastx.tsv; Input files updated by another job: /home/Documents/coregenomeprimers/last/CoreGenomePrimers/tests/tmp/cabana/CoreGenomePrimers_2359642/blastx_nontarget/hits.txt
resources: tmpdir=/tmp, time=59, mem_gb_pt=50
[Sun Sep 25 03:59:09 2022]
Finished job 21.
72 of 151 steps (48%) done
Removing temporary output /home/Documents/coregenomeprimers/last/CoreGenomePrimers/tests/tmp/cabana/CoreGenomePrimers_2359642/blastx_nontarget/hits.txt.
BUG: Out of jobs ready to be started, but not all files built yet. Please check snakemake/snakemake#823 for more information.
Remaining jobs:
Pipeline failed! Creating report...
What is the best option to solve this bug? Because the link snakemake/snakemake#823 is confused. I am using snakemake 7.14.0
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