Prokka setupdb issue

Question

[DanielC]

Dear Friends,

I am trying to annotate an assembled phage genome using prokka. I made a hmm model using VFAM and adding some protein sequences specific to my phage. I paced the hmm to the path where the prokka databases are. In my case the database path is:

/data/deepak-data/softwares/prokka/prokka/db

I installed prokka by following the instructions from https://github.com/tseemann/prokka

My system is Centos. After setting up I ran this command:

prokka --dbdir C600S -phage --prefix C600 -phage --addgenes --addmrna --locustag C600s --compliant --genus Staphylococcus --species phage --strain C600 --kingdom Viruses --gcode 11 --usegenus --proteins vFam-B_2014_inProfiles-with-C600-20_blasthits.fasta -hmms vFam-B_2014_inProfiles-with-C600-20_blasthits.hmm --metagenome --rawproduct ---mincontiglen 200 --rfam

When running the above command I get this error below:

[02:21:09] This is prokka 1.13.3
[02:21:09] Written by Torsten Seemann <[e-mail]>
[02:21:09] Homepage is https://github.com/tseemann/prokka
[02:21:09] Local time is Wed Apr  3 02:21:09 2019
[02:21:09] You are root
[02:21:09] Operating system is linux
[02:21:09] You have BioPerl 1.007002
[02:21:09] System has 20 cores.
[02:21:09] Will use maximum of 8 cores.
[02:21:09] Annotating as >>> Viruses <<<
[02:21:09] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.

To solve the above issue, I did 'prokka --setupdb' and got this:

[13:47:34] Looking for 'makeblastdb' - found /root/miniconda2/bin/makeblastdb
[13:47:34] Determined makeblastdb version is 2.7
[13:47:34] Making kingdom BLASTP database: /root/miniconda2/db/kingdom/Archaea/sprot
[13:47:34] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/kingdom\/Archaea\/sprot -logfile /dev/null
[13:47:34] Making kingdom BLASTP database: /root/miniconda2/db/kingdom/Bacteria/sprot
[13:47:34] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/kingdom\/Bacteria\/sprot -logfile /dev/null
[13:47:36] Making kingdom BLASTP database: /root/miniconda2/db/kingdom/Mitochondria/sprot
[13:47:36] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/kingdom\/Mitochondria\/sprot -logfile /dev/null
[13:47:36] Making kingdom BLASTP database: /root/miniconda2/db/kingdom/Viruses/sprot
[13:47:36] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/kingdom\/Viruses\/sprot -logfile /dev/null
[13:47:36] Making kingdom BLASTP database: /root/miniconda2/db/kingdom/Bacteria/IS
[13:47:36] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/kingdom\/Bacteria\/IS -logfile /dev/null
[13:47:37] Making kingdom BLASTP database: /root/miniconda2/db/kingdom/Bacteria/AMR
[13:47:37] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/kingdom\/Bacteria\/AMR -logfile /dev/null
[13:47:37] Making genus BLASTP database: /root/miniconda2/db/genus/Enterococcus
[13:47:37] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/genus\/Enterococcus -logfile /dev/null
[13:47:38] Making genus BLASTP database: /root/miniconda2/db/genus/Escherichia
[13:47:38] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/genus\/Escherichia -logfile /dev/null
[13:47:38] Making genus BLASTP database: /root/miniconda2/db/genus/Staphylococcus
[13:47:38] Running: makeblastdb -hash_index -dbtype prot -in \/root\/miniconda2\/db\/genus\/Staphylococcus -logfile /dev/null
[13:47:38] Looking for 'hmmpress' - found /root/miniconda2/bin/hmmpress
[13:47:38] Determined hmmpress version is 3.2
[13:47:38] Pressing HMM database: /root/miniconda2/db/hmm/HAMAP.hmm
[13:47:38] Running: hmmpress \/root\/miniconda2\/db\/hmm\/HAMAP\.hmm
Working...    done.
Pressed and indexed 1463 HMMs (1463 names).
Models pressed into binary file:   /root/miniconda2/db/hmm/HAMAP.hmm.h3m
SSI index for binary model file:   /root/miniconda2/db/hmm/HAMAP.hmm.h3i
Profiles (MSV part) pressed into:  /root/miniconda2/db/hmm/HAMAP.hmm.h3f
Profiles (remainder) pressed into: /root/miniconda2/db/hmm/HAMAP.hmm.h3p
[13:47:40] Pressing HMM database: /root/miniconda2/db/hmm/VFAM.hmm
[13:47:40] Running: hmmpress \/root\/miniconda2\/db\/hmm\/VFAM\.hmm
Working...    done.
Pressed and indexed 5344 HMMs (5344 names).
Models pressed into binary file:   /root/miniconda2/db/hmm/VFAM.hmm.h3m
SSI index for binary model file:   /root/miniconda2/db/hmm/VFAM.hmm.h3i
Profiles (MSV part) pressed into:  /root/miniconda2/db/hmm/VFAM.hmm.h3f
Profiles (remainder) pressed into: /root/miniconda2/db/hmm/VFAM.hmm.h3p
[13:48:01] Looking for 'cmpress' - found /root/miniconda2/bin/cmpress
[13:48:01] Determined cmpress version is 1.1
[13:48:01] Pressing CM database: /root/miniconda2/db/cm/Viruses
[13:48:01] Running: cmpress \/root\/miniconda2\/db\/cm\/Viruses
Working...    done.
Pressed and indexed 142 CMs and p7 HMM filters (142 names and 142 accessions).
Covariance models and p7 filters pressed into binary file:  /root/miniconda2/db/cm/Viruses.i1m
SSI index for binary covariance model file:                 /root/miniconda2/db/cm/Viruses.i1i
Optimized p7 filter profiles (MSV part)  pressed into:      /root/miniconda2/db/cm/Viruses.i1f
Optimized p7 filter profiles (remainder) pressed into:      /root/miniconda2/db/cm/Viruses.i1p
[13:48:01] Pressing CM database: /root/miniconda2/db/cm/Bacteria
[13:48:01] Running: cmpress \/root\/miniconda2\/db\/cm\/Bacteria
Working...    done.
Pressed and indexed 1027 CMs and p7 HMM filters (1027 names and 1027 accessions).
Covariance models and p7 filters pressed into binary file:  /root/miniconda2/db/cm/Bacteria.i1m
SSI index for binary covariance model file:                 /root/miniconda2/db/cm/Bacteria.i1i
Optimized p7 filter profiles (MSV part)  pressed into:      /root/miniconda2/db/cm/Bacteria.i1f
Optimized p7 filter profiles (remainder) pressed into:      /root/miniconda2/db/cm/Bacteria.i1p
[13:48:02] Looking for databases in: /root/miniconda2/db
[13:48:02] * Kingdoms: Archaea Bacteria Bacteria Bacteria Mitochondria Viruses
[13:48:02] * Genera: Enterococcus Escherichia Staphylococcus
[13:48:02] * HMMs: HAMAP VFAM
[13:48:02] * CMs: Bacteria Viruses

I see that for some reason the prokka database is taken from " /root/miniconda2/db/" where the prokka database is at " /data/deepak-data/softwares/prokka/prokka/db"; I think the issue is arising because of this, so I copied the generated files after "prokka --setupdb" from " /root/miniconda2/db/" to "/data/deepak-data/softwares/prokka/prokka/db" and then ran the prokka command line again but got the same error:

[02:21:09] This is prokka 1.13.3
[02:21:09] Written by Torsten Seemann [e-mail]
[02:21:09] Homepage is https://github.com/tseemann/prokka
[02:21:09] Local time is Wed Apr 3 02:21:09 2019
[02:21:09] You are root
[02:21:09] Operating system is linux
[02:21:09] You have BioPerl 1.007002
[02:21:09] System has 20 cores.
[02:21:09] Will use maximum of 8 cores.
[02:21:09] Annotating as >>> Viruses <<<
[02:21:09] The sequence databases have not been indexed. Please run 'prokka --setupdb' first.

Could you please guide me on how to resolve this issue? I would really appreciate. Thank you for your time.

Thanks,

[Bastien Hervé]

I paced the hmm to the path where the prokka databases are. In my case the database path is:

/data/deepak-data/softwares/prokka/prokka/db

Could you confirm this typing :

prokka --listdb

please, share the output

[DanielC]

I did this and got:

prokka --listdb

[15:20:19] Looking for databases in: /root/miniconda2/db
[15:20:19] * Kingdoms: Archaea Bacteria Bacteria Bacteria Mitochondria Viruses
[15:20:19] * Genera: Enterococcus Escherichia Staphylococcus
[15:20:19] * HMMs: HAMAP VFAM
[15:20:19] * CMs: Bacteria Viruses

Answer 1

[DanielC]

I figured out the issue...I put "--dbdir" in the command line instead of "--outdir". It ran successfully. Thanks for your replies and time.