no rRNA prediction using Barrnap

[gaworj]

Hi,

Thank you very much for great tool!

I have encountered error when using DFAST for rRNA prediction - no rRNA genes in output.

DFAST was run in debug mode and this is my barrnap log output:

[barrnap] This is barrnap 0.9
[barrnap] Written by Torsten Seemann
[barrnap] Obtained from https://github.com/tseemann/barrnap
[barrnap] Detected operating system: linux
[barrnap] Adding /home/jang/anaconda3/envs/mamba/envs/dfast-1-2-18/lib/barrnap/bin/../binaries/linux to end of PATH
[barrnap] Checking for dependencies:
[barrnap] Found nhmmer - /home/jang/anaconda3/envs/mamba/envs/dfast-1-2-18/bin/nhmmer
[barrnap] Found bedtools - /home/jang/anaconda3/envs/mamba/envs/dfast-1-2-18/bin/bedtools
[barrnap] Will use 1 threads
[barrnap] Setting evalue cutoff to 1e-06
[barrnap] Will tag genes < 0.8 of expected length.
[barrnap] Will reject genes < 0.25 of expected length.
[barrnap] Using database: /home/jang/anaconda3/envs/mamba/envs/dfast-1-2-18/lib/barrnap/bin/../db/bac.hmm
[barrnap] Scanning 96K_ref_3x_DFAST_v1/input/genome.fna for bac rRNA genes... please wait
[barrnap] Command: nhmmer --cpu 1 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/home/jang/anaconda3/envs/mamba/envs/dfast-1-2-18/lib/barrnap/bin/../db/bac.hmm' '96K_ref_3x_DFAST_v1/input/genome.fna'
[barrnap] ERROR: nhmmer failed to run - Error: Invalid alphabet type in target for nhmmer. Expect DNA or RNA.

Any hints?

Bests,
Jan

[nigyta]

Thank you for using DFAST.
I found the same issue here, tseemann/barrnap#54

Does your genome sequence contain any ambiguous bases such as Y (C or T) or R (A or G)?

[gaworj]

I have run DFAST on multiple complete genome assemblies. Tried different DFAST versions and still there were no rRNA operons predicted.
Interestingly I did one another test today: run barrnap in my DFAST conda env. Everything works fine.

[gaworj]

OK. I did some tests on my side and have interesting observation. I have noticed that sometimes DFAST is changing input fasta file header in his working directory to empty line and then barrnap is not working properly.

Finally I found the solution:

I have unfortunately run DFAST with "--complete t" option without adding "--seq_names my_genome" parameter.

This is my final proper command:

dfast -g test_chromosome_v1.fas -o test_chromosome_refs_3x_DFAST_020323 --db /home/jang/data_HDD1/dfast_db/ --cpu 12 --debug --references 'ref1_sequence.gb;ref2_sequence.gb;ref3_sequence.gb' --locus_tag_prefix test_locus --center_name IBB_PAS --organism Acinetobacter_baumannii --strain my_test --complete t --seq_names test_chromosome