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:zap: :aquarius: Rapid prokaryotic genome annotation
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'Could not run command' for custom HMM database #195

Closed MattPinder closed 8 years ago

MattPinder commented 8 years ago

I downloaded a custom HMM database for use with Prokka (specifically, the TIGR database), and subsequently ran hmmpress and --setupdb on it before running Prokka; however, the job does not complete, and when I check the log file, it seems to get stuck on my custom database. I have tried with and without the --hmms option, but the result is the same. Below is the result when I run Prokka with the --hmms option:

[10:48:55] Preparing user-supplied primary HMMER annotation source: /db/prokka/hmm/TIGR.hmm
[10:48:55] Using /inference source as 'TIGR'
[10:48:55] Annotating CDS, please be patient.
[10:48:55] Will use 8 CPUs for similarity searching.
[10:49:09] There are still 4686 unannotated CDS left (started with 4686)
[10:49:09] Will use hmmer3 to search against /db/prokka/hmm/TIGR.hmm with 8 CPUs
[10:49:09] Running: cat PROKKA_Test_1\.6\/TIGR\.hmm\.faa | parallel --gnu --plain -j 8 --block 102881 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /db/prokka/hmm/TIGR.hmm /dev/stdin > PROKKA_Test_1\.6\/TIGR\.hmm\.hmmer3 2> /dev/null
[10:49:10] Could not run command: cat PROKKA_Test_1\.6\/TIGR\.hmm\.faa | parallel --gnu --plain -j 8 --block 102881 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /db/prokka/hmm/TIGR.hmm /dev/stdev/stdin > PROKKA_Test_1\.6\/TIGR\.hmm\.hmmer3 2> /dev/null

Any help on getting this running would be greatly appreciated!

tseemann commented 8 years ago

Are you using latest Prokka HEAD? What does prokka --version say? Can you send the prokka.log files?

MattPinder commented 8 years ago

I'm using Prokka 1.12-beta, which fixed my previous issue. I have attached the log file for the failed job; apologies if this is not the file you were asking for, I couldn't find a file explicitly called prokka.log. PROKKA_Test_1.6.txt

MattPinder commented 8 years ago

After double-checking some files on my system, I now see that the problem was human error on my own part, having incorrectly propagated the new database files; Prokka now appears to be working exactly as it should. Apologies.

tseemann commented 8 years ago

Glad you got it working @MattPinder