Could not run command: tbl2asn

[tallnuttcsiro]

Hi,
getting this error, not sure why, it seems to find tbl2asn ok. Here's the log file,

Thanks.

[11:17:34] Command: --force --outdir 3-scaffold13 --prefix 3-scaffold13 --locustag 3-scaffold13 --cpus 0 --metagenome --mincontiglen 200 --norrna --notrna 3-scaffold13.fasta
[11:17:34] Looking for 'aragorn' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/aragorn
[11:17:34] Determined aragorn version is 1.2
[11:17:34] Looking for 'barrnap' - found /usr/local/bin/barrnap
[11:17:34] Determined barrnap version is 0.6
[11:17:34] Looking for 'blastp' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/blastp
[11:17:34] Determined blastp version is 2.2
[11:17:34] Looking for 'cmpress' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/cmpress
[11:17:34] Determined cmpress version is 1.1
[11:17:34] Looking for 'cmscan' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/cmscan
[11:17:34] Determined cmscan version is 1.1
[11:17:34] Looking for 'egrep' - found /bin/egrep
[11:17:34] Looking for 'find' - found /usr/bin/find
[11:17:34] Looking for 'grep' - found /bin/grep
[11:17:34] Looking for 'hmmpress' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/hmmpress
[11:17:34] Determined hmmpress version is 3.1
[11:17:34] Looking for 'hmmscan' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/hmmscan
[11:17:34] Determined hmmscan version is 3.1
[11:17:34] Looking for 'less' - found /usr/bin/less
[11:17:34] Looking for 'makeblastdb' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/makeblastdb
[11:17:34] Determined makeblastdb version is 2.2
[11:17:34] Looking for 'minced' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/bin/../binaries/linux/../common/minced
[11:17:34] Determined minced version is 1.6
[11:17:34] Looking for 'parallel' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/bin/../binaries/linux/../common/parallel
[11:17:34] Determined parallel version is 20150122
[11:17:34] Looking for 'prodigal' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/prodigal
[11:17:34] Determined prodigal version is 2.6
[11:17:34] Looking for 'prokka-genbank_to_fasta_db' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/bin/prokka-genbank_to_fasta_db
[11:17:34] Looking for 'rnammer' - found /OSM/HOME-MEL/all29c/bin/rnammer
[11:17:35] Determined rnammer version is 1.2
[11:17:35] Looking for 'sed' - found /bin/sed
[11:17:35] Looking for 'tbl2asn' - found /OSM/HOME-MEL/all29c/bin/prokka-1.11/binaries/linux/tbl2asn
[11:17:35] Determined tbl2asn version is 23.2
[11:17:35] Using genetic code table 11.
[11:17:35] Loading and checking input file: 3-scaffold13.fasta
[11:17:35] Wrote 4 contigs
[11:17:35] Skipping tRNA search at user request.
[11:17:35] Disabling rRNA search: --kingdom=Bacteria or --norrna=1
[11:17:35] Skipping ncRNA search, enable with --rfam if desired.
[11:17:35] Total of 0 tRNA + rRNA features
[11:17:35] Searching for CRISPR repeats
[11:17:35] Found 0 CRISPRs
[11:17:35] Predicting coding sequences
[11:17:35] Contigs total 85242 bp, so using meta mode
[11:17:35] Running: prodigal -i 3-scaffold13/3-scaffold13.fna -c -m -g 11 -p meta -f sco -q
[11:17:36] Found 67 CDS
[11:17:36] Connecting features back to sequences
[11:17:36] Not using genus-specific database. Try --usegenus to enable it.
[11:17:36] Annotating CDS, please be patient.
[11:17:36] Will use 30 CPUs for similarity searching.
[11:17:36] There are still 67 unannotated CDS left (started with 67)
[11:17:36] Will use blast to search against /OSM/HOME-MEL/all29c/bin/prokka-1.11/bin/../db/kingdom/Bacteria/sprot with 30 CPUs
[11:17:36] Running: cat 3-scaffold13/sprot.faa | parallel --gnu --plain -j 30 --block 400 --recstart '>' --pipe blastp -query - -db /OSM/HOME-MEL/all29c/bin/prokka-1.11/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > 3-scaffold13/sprot.blast 2> /dev/null
[11:17:37] Modify product: Probable L,D-transpeptidase YbiS precursor => putative L,D-transpeptidase YbiS precursor
[11:17:37] Modify product: Uncharacterized oxidoreductase YbiC => putative oxidoreductase YbiC
[11:17:37] Modify product: Probable outer membrane usher protein ElfC precursor => putative outer membrane usher protein ElfC precursor
[11:17:37] Modify product: Probable diguanylate cyclase YcdT => putative diguanylate cyclase YcdT
[11:17:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS
[11:17:37] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986/MT1014 => putative ABC transporter ATP-binding protein/MT1014
[11:17:37] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase
[11:17:37] Modify product: Probable ATP-dependent helicase DinG => putative ATP-dependent helicase DinG
[11:17:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YbhF => putative ABC transporter ATP-binding protein YbhF
[11:17:38] Cleaned 9 /product names
[11:17:38] Deleting unwanted file: 3-scaffold13/sprot.faa
[11:17:38] Deleting unwanted file: 3-scaffold13/sprot.blast
[11:17:38] Labelling remaining 14 proteins as 'hypothetical protein'
[11:17:38] Found 49 unique /gene codes.
[11:17:38] Fixed 2 duplicate /gene - ecpD_1 ecpD_2
[11:17:38] Fixed 2 duplicate /gene - bhsA_1 bhsA_2
[11:17:38] Fixed 2 colliding /gene names.
[11:17:38] Adding /locus_tag identifiers
[11:17:38] Assigned 67 locus_tags to CDS and RNA features.
[11:17:38] Writing outputs to 3-scaffold13/
[11:17:38] Generating annotation statistics file
[11:17:38] Generating Genbank and Sequin files
[11:17:38] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.11 from http://www.vicbioinformatics.com' -Z 3-scaffold13/3-scaffold13.err -i 3-scaffold13/3-scaffold13.fsa 2> /dev/null
[11:17:38] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.11 from http://www.vicbioinformatics.com' -Z 3-scaffold13/3-scaffold13.err -i 3-scaffold13/3-scaffold13.fsa 2> /dev/null

[tseemann]

Your copy of tbl2asn has expired (NCBI enforces this, not me!).

You need to replace it with the latest version. You can download it from https://github.com/tseemann/prokka/raw/master/binaries/linux/tbl2asn

[sorenwacker]

And what should we do with that file??
Under linux type which tbl2asn. There should the location of the file that you are currently using. If you run that file, it probably says something like, this file is older than a year, you need a new version. So, replace that file the downloaded version. And you should be fine.

[microbioticajon]

Hi @tseemann

Appreciate this is not your doing but would it be possible to put a note (preferably in blinking red text) next to this dependency in the README about this feature??

I can see there is a note in the FAQ but it implies you have already been affected by the problem rather than letting you know about it before you start /:)

Best,
J

[cssulliv]

Hi,

I encountered the same issue when I ran prokka v1.14.5 (downloaded via conda) on our university server. Once the .dms file is downloaded how do I exactly integrate it (ie where should it be saved, do I need to alter code) so that tbl2asn doesn't fail?

[YePererva]

Just in case if anybody would need "instructions":

• By default, the tbl2asn is "installed" to $home/prokka/binaries/linux/tbl2asn
• The fresh version of tbl2asn I found here

To make an upgrade of binary:

# remove old file
rm -f $home/prokka/binaries/linux/tbl2asn
# download the new file as archive
wget https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
# unpack the archive
gunzip ./linux64.tbl2asn.gz
# move / copy the binary to the target location 
# or to any other location within $PATH variable
# may require sudo depending on your location
mv ./linux64.tbl2asn $home/prokka/binaries/linux/tbl2asn
# add permission to execute
sudo chmod +x $home/prokka/binaries/linux/tbl2asn

After those actions, I didn't encounter the error anymore.

@sorenwacker: For some reason which tbl2asn doesn't show the location of tbl2asn if installed with conda

[Adarsh931]

In case anyone is still facing error even after downloading a fresh tbl2asn file (from NCBI: [https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/]) and placing it in prokka/binaries/linux directory, try making it executable using chmod +x tbl2asn. Doing this worked for me.

[zagrosman]

Dear @tseemann

Thanks in advance for your continued support on this page. I checked all the answers posted here and I think the solution is clear. Prokka users can run the following commands to upgrade tbl2asn to the latest version and then run Prokka.

1- sudo apt-get update -y
and
2- sudo apt-get install -y ncbi-tools-bin

By default, Prokka searches /usr/bin folder to find tbl2asn module.