Error in process Trinotate.

[ghost]

Hi Ramon, I run full pipeline by foolowing command.

nextflow run TransPi.nf --all --reads /path/to/Read_R[1,2].fastq.gz --k 25,41,53,75 --maxReadLen 100 --outdir transpi-out -w transpi-wd --tracedir transpi-info -profile docker --allBuscos --skipQC --skipFilter --rescueBusco --buscoDist

And I got an error in process trinotate. My .command.out from process trinotate is this.

-- Running Trinotate --

memory
memory

-- Ending run of Trinotate --


-- Loading hits and predictions to sqlite database... --

memory
memory
memory
memory
memory
No transmembrane domains (tmhmm)
No Signal-P
No rnammer results

-- Loading finished --


-- Generating report... --


-- Report generated --


-- Creating GO file from XLS... --


-- Done with the GO --


-- Creating KEGG file from XLS... --


-- Done with the KEGG --


-- Creating eggNOG file from XLS... --

Since there is no output after the following process (e.g. the message "Done with the eggNOG"), I thought there was a problem with this command. However, when I ran this command in a different terminal, no error occurred.

cat Read_R.trinotate_annotation_report.xls | cut -f 1,13 | grep "OG" | tr "\`" ";" | sed 's/^/#/g' | sed 's/;/\n;/g' | cut -f 1 -d "^" | tr -d "\n" | tr "#" "\n" | grep "OG" >Read_R.eggNOG_COG.terms.txt

Is there any reason for this error? My TransPi version is v1.3.0-rc. Thank you.

[rivera10]

Hello @HarukiNakamura,

When running the command you mentioned

cat Read_R.trinotate_annotation_report.xls | cut -f 1,13 | grep "OG" | tr "\`" ";" | sed 's/^/#/g' | sed 's/;/\n;/g' | cut -f 1 -d "^" | tr -d "\n" | tr "#" "\n" | grep "OG" >Read_R.eggNOG_COG.terms.txt

you get the file with the info of eggNOG or the file is empty?

Best, Ramon

[ghost]

I got an empty file.

[rivera10]

Interesting. Could I see your XLS file that was generated by Trinotate? That way I can troubleshoot and see why the code is not working. My email is r.rivera /@/ lrz.uni-muenchen.de. Thanks

[ghost]

Thanks for your reply. I can attach herewith.

Read_R.trinotate_annotation_report.xls

I have checked my Trinotarte.sqlite and it seems to be working properly until perhaps the data is loaded.