Error updating Kraken2 GTDB Database with MAGs - MissingOutputException in rule kraken2_cp_to_tmp in file

[PeterCx]

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

[PeterCx]

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