PeterCx
commented
1 year ago There was an error in the config file.
Saved databases that will be updated
kraken2_db: library: /workspace/pot/peterc/Equine/Struo2/custom_dbs taxonomy: /workspace/pot/peterc/Equine/Struo2/custom_dbs
Should be:
kraken2_db: library: /workspace/pot/peterc/Equine/Struo2/custom_dbs/library taxonomy: /workspace/pot/peterc/Equine/Struo2/custom_dbs/taxonomy
Many thanks
Hi Nick,
I am encountering a problem when using snakemake to update my Kraken2 database. See the error bwlo.
Waiting at most 5 seconds for missing files. MissingOutputException in rule kraken2_cp_to_tmp in file /workspace/pot/peterc/Equine/Struo2/bin/ Job 2 completed successfully, but some output files are missing. Missing files after 5 seconds. is the case, consider to increase the wait time with --latency-wait: tmp/db_update_tmp/peterc/Struo2_112566273/db_update/kraken2/taxonomy/nodes.dmp tmp/db_update_tmp/peterc/Struo2_112566273/db_update/kraken2/taxonomy/names.dmp Removing output files of failed job kraken2_cp_to_tmp since they might be corrupted: tmp/db_update_tmp/peterc/Struo2_112566273/db_update/kraken2/library, tmp/db_update_tmp/peterc/Str Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message
Pipeline failed! Creating report... --- I/O info --- tmp_dir: tmp/db_update_tmp/peterc/Struo2_112566273/ % used size: 82.1 % used inodes: 0.0 output_dir: /workspace/pot/peterc/Equine/Struo2/Output/ % used size: 82.1 % used inodes: 0.0 --- Summarizing job logs --- 2023-01-27 14:10:17,527 - Parsing log: /workspace/pot/peterc/Equine/Struo2/.snakemake/log/2023-01-27T133338.647415.snakemake.log 2023-01-27 14:10:17,873 - Cannot find qacct log: /var/lib/gridengine/default/common/accounting; Skipping --- No email provided; not sending a notification --- Complete log: .snakemake/log/2023-01-27T133338.647415.snakemake.log
I cant detect what the exact problem is. See attached the files associated with this. I am using the following command to run the pipeline:
snakemake --use-conda --cores 20 --configfile config-update.yaml
job_report.csv config-update.txt Sample_Table.txt
Your help is greatly appreciated.
Kind regards,
P