kracken2/bracken output files integrity check
Hi everyone,
I just ran Kraken2 and Bracken on a large metagenomics dataset on a SLURM cluster, and since some jobs might have suffered from silent memory crashes or timeouts, I'd like to make sure none of the output files were truncated or corrupted due to memory issues, timeouts, or failed jobs.
Are there any recommended bioinformatic tools or workflows for checking the integrity and completeness of Kraken2/Bracken output files ?
Thanks for your help!
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Instead of output files, take a look at the SLURM job log files. If any job had an issue that should be captured in the log files. If you can find warnings/errors then the outputs for those jobs would likely be suspect.
Otherwise simply move forward with your analysis and see if there are any failures downstream with file reads etc.