DIAMOND task failed

[Carmen Chen]

Hi,

It is my first time using checkV. I followed the instructions to install via conda and downloaded the database. However, I am running into an issue when I try to run checkv completeness. I get the error: DIAMOND task failed. Program should be rerun.

CheckV v1.0.1: completeness
[1/8] Skipping gene calling...
[2/8] Initializing queries and database...
[3/8] Running DIAMOND blastp search...
DIAMOND task failed. Program should be rerun.

Do you have any suggestions on how to resolve this issue?

Many thanks!

Carmen

[Stephen Nayfach]

I thought I replied to this earlier, but looking now I don’t see my message… Can you send me the log file from the tmp directory: /path/to/output/tmp/diamond.log

[Carmen Chen]

Hi Stephen,

Thank you for the quick reply!

The log says “Error: Database was built with a different version of diamond as is incompatible.”

This is after I installed with the versions listed in your instructions (conda create -n checkv diamond=2.0.4 hmmer=3.3 prodigal-gv=2.6.3).

The database was built using checkv download_database ./

Thank you!

[Stephen Nayfach]

Hmm that’s strange. Quick fix would be to build the database manually. You can cd /path/to/checkvdb/genome_db and then run diamond using the installed version diamond makedb --in checkv_reps.faa --db checkv_reps Otherwise I’d suggest reinstalling using just conda install -c bioconda checkv

[Carmen Chen]

Hi Stephen,

That solved my issue (diamond makedb --in checkv_reps.faa --db checkv_reps) and I can run checkv completely now.

Thank you so much!(:

Carmen

[Stephen Nayfach]

Welcome!