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SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
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Error with DIAMOND Database #48

Closed mweberr closed 4 years ago

mweberr commented 4 years ago

The master script stops after the ribo-depletion step with error

Error: Database file is not a DIAMOND database.

'diamond blastx --db samsa2/full_databases/RefSeq_bac -q samsa2/step_3_output/test.merged.ribodepleted.fastq -a test.merged.ribodepleted.fastq.RefSeq -t ./ -k 1' exited with non-zero status 1

Do I have to convert the RefSeq_bac to DIAMOND format ?

Thanks for you help!

transcript commented 4 years ago

Hi there,

Yes, you've got the nail on the head - the RefSeq_bac database will need to be in DIAMOND-compressed format.

You can do this by running:

diamond makedb --in RefSeq_bac -d RefSeq_bac_dmnd

Be sure to supply the DIAMOND-compressed database for step 4, but use the regular (plain-text) database for step 5, when you get the nice summary of results.

Best, Sam