How to run Trinotate

Question

[luzglongoria]

Hi,

I need to use Trinotate for finishing my transcriptomic analyses. I have followed the instructions in :

https://github.com/Trinotate/Trinotate.github.io/wiki

I am in the step called ' Automated Execution of Trinotate: Running computes and loading results' . Apart from running Trinotate itself, I am not sure what I need to do exactly. If I understand correctly the instructions, I need to modify the headers of a file called 'conf.txt' that it is in /auto/conf.txt

BUT I don't find this file anywhere.

I have been googling and found this:

https://github.com/Trinotate/Trinotate/blob/master/auto/conf.txt

where it explains what is this conf.txt file and what contains.

My questions are:

1 . Do I need to create a file like this: ?

nano conf.txt

with all the info from https://github.com/Trinotate/Trinotate/blob/master/auto/conf.txt and modify the headers (i.e where to find each file).

2 . Do I need to modify the autoTrinotate.pl?

3 . For running Trinotate the command would be:

runMe.sh autoTrinotate.pl

right?

Maybe they are very basic questions but I want to be sure that I understand all the steps.

Thank you in advance.

[luzglongoria]

Thank you so much h.mon for your answer.

However, I get an error message when I try to run the command for Trinotate.

I have create a conf.txt file that looks like:

# progs
TRANSDECODER_DIR=/home/luz_garcia_longoria/miniconda3/pkgs/transdecoder-5.5.0-0
BLASTX_PROG=/home/luz_garcia_longoria/miniconda3/pkgs/blast-2.7.1-h4422958_6
BLASTP_PROG=/home/luz_garcia_longoria/miniconda3/pkgs/blast-2.7.1-h4422958_6
HMMSCAN_PROG=/home/luz_garcia_longoria/miniconda3/pkgs/hmmer-3.2.1-hf484d3e_1

#dbs
SWISSPROT_PEP=/home/luz_garcia_longoria/workspace/Trinonate/uniprot_sprot.pep
PFAM_DB=/home/luz_garcia_longoria/workspace/Trinonate/Pfam-A.hmm

####################
#  BioIfx computes  ** no need to edit the commands below **
####################

[TRANSDECODER_LONGORF]
RANK=100
RUN=T
CMD={__TRANSDECODER_DIR__}/TransDecoder.LongOrfs -t {__TRANSCRIPTS_FASTA__}

[TRANSDECODER_PREDICT]
RANK=101
RUN=T
CMD={__TRANSDECODER_DIR__}/TransDecoder.Predict -t {__TRANSCRIPTS_FASTA__} --cpu {__CPU__}

[BLASTX_SPROT_TRANS]
RANK=200
RUN=T
CMD={__BLASTX_PROG__} -db {__SWISSPROT_PEP__} -query {__TRANSCRIPTS_FASTA__} -num_threads {__CPU__} -
max_target_seqs 1 -outfmt 6 -evalue 1e-5 > swissprot.blastx.outfmt6

[BLASTX_SPROT_PEP]
RANK=300
RUN=T
CMD={__BLASTP_PROG__} -query {__TRANSCRIPTS_FASTA__}.transdecoder.pep -db {__SWISSPROT_PEP__} -num_threads
 {__CPU__}  -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > swissprot.blastp.outfmt6

[PFAM]
RANK=400
RUN=T
CMD={__HMMSCAN_PROG__} --cpu {__CPU__} --domtblout TrinotatePFAM.out {__PFAM_DB__} 
{__TRANSCRIPTS_FASTA__}.transdecoder.pep  > pfam.log

#############################
# Trinotate Database Loading
#############################

[TRINOTATE_INIT]
RANK=1100
RUN=T
CMD=Trinotate {__TRINOTATE_SQLITE__} init --gene_trans_map {__GENE_TO_TRANS_MAP__} --transcript_fasta 
{__TRANSCRIPTS_FASTA__} --transdecoder_pep {__TRANSCRIPTS_FASTA__}.transdecoder.pep

[TRINOTATE_LOAD_SPROT_BLASTX]
RANK=1200
RUN=T
CMD=Trinotate  {__TRINOTATE_SQLITE__} LOAD_swissprot_blastx swissprot.blastx.outfmt6

[TRINOTATE_LOAD_SPROT_BLASTP]
RANK=1300
RUN=T
CMD=Trinotate  {__TRINOTATE_SQLITE__} LOAD_swissprot_blastp swissprot.blastp.outfmt6

[TRINOTATE_LOAD_PFAM]
RANK=1400
RUN=T
CMD=Trinotate  {__TRINOTATE_SQLITE__} LOAD_pfam TrinotatePFAM.out

[TRINOTATE_REPORT]
RANK=1800
RUN=T
CMD=Trinotate  {__TRINOTATE_SQLITE__} report > Trinotate.xls

[EXTRACT_GO]
RANK=1900
RUN=T
CMD=extract_GO_assignments_from_Trinotate_xls.pl  --Trinotate_xls Trinotate.xls -T -I > Trinotate.xls.gene_ontology

[NAME_UPDATES]
RANK=2000
RUN=T
CMD=import_transcript_names.pl {__TRINOTATE_SQLITE__} Trinotate.xls

I have run the following command:

 autoTrinotate.pl
 --Trinotate_sqlite Trinotate.sqlite
 --transcripts trinity_low_CG.fa
 --gene_to_trans_map Trinity.fasta.gene_trans_map
 --conf conf.txt --CPU 12

and the error that I get is:

Error, no section values recorded for GLOBALS at /home/luz_garcia_longoria/miniconda3/envs/salmon/lib/site_perl/5.26.2/IniReader.pm line 117.
IniReader::get_section_hash(IniReader=HASH(0x1056fb0), "GLOBALS") called at /home/luz_garcia_longoria/miniconda3/envs/salmon/bin/autoTrinotate.pl line 74

I think I have specified all the resource locations and other templated parameter values, as requested. The directory where I run the command is:

/home/luz_garcia_longoria/workspace/Trinonate

Any guess why I get this error?

Thank you

[h.mon]

It seems the conf.txt example starts with [GLOBALS], and yours don't:

[GLOBALS]
#  ** edit the progs and dbs section to point to your local resources.
# progs
TRANSDECODER_DIR=/home/unix/bhaas/GITHUB/TransDecoder
BLASTX_PROG=blastx
BLASTP_PROG=blastp

If this doesn't solve the problem, you can still run all necessary steps separately instead of using the autoTrinotate.pl script. Or you can write to the Trinotate mailing list:

https://groups.google.com/forum/?hl=en#!forum/trinotate-users

Answer 1

[h.mon]

1) yes

2) no

3) no, you run like this:

$TRINOTATE_HOME/auto/autoTrinotate.pl --Trinotate_sqlite <string> \
       --transcripts <string> \
      --gene_to_trans_map <string> \
       --conf <string> \
       --CPU <int>

runMe.sh just run the pipeline with the example files.

[luzglongoria]

Thank you so much for your answer. I will try like this :)