A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi,
I'm getting an error from PROKKA when I use commits `6f837de` and `0c765e6`:
&gt; Could not run command: cat P6071_515_bin283\/P6071_515_bin283\.AMR\.tmp\.43\.faa | parallel --gnu --plain -j 2 --block 128441 --recstart '&gt;' --pipe blastp -query - -db /usr/local/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no &gt; P6071_515_bin283\/P6071_515_bin283\.AMR\.tmp\.43\.blast 2&gt; /dev/null
the same MAG completes without errors on commit `6a5be81`. As far as I can tell nothing has changed in terms of genome fasta or prokka versions.

The only possible error I can imagine from `cat` is that the disk is full (or too many files if it's Dardel). (Pity that stderr is redirected.)

Forget that, it's of course not `cat` that's causing the problem... I would `cd` into the work directory and see if I can run Prokka manually. (Running the above command on its own won't work, I guess, because of the path to the db.)

Another thing: Did you remember to `-resume`? Since we haven't updated the Prokka module, Nextflow should see that this is already done. After the error above, this is too late now however.