brianjohnhaas
commented
5 years ago Hi Charles,
If you can send me your annotation xls file you're using as the input to this, I'll debug it directly.
bhaas@broadinstitute.org
many thx,
~brian
On Wed, Feb 13, 2019 at 10:17 PM charlesfoster notifications@github.com wrote:
Hi,
I've successfully generated an annotation file using the Trinotate pipeline. For GO enrichment with GOseq, I wish to create a file with GO annotations mapped to genes. The Trinotate wiki indicates that this can be done with the script extract_GO_assignments_from_Trinotate_xls.pl. As per the instructions, I ran the following:
${TRINOTATE_HOME}/util/extract_GO_assignments_from_Trinotate_xls.pl --Trinotate_xls annotation.xls --G --include_ancestral_terms > go_annotations.txt
It's starts off fine, like so:
Total transcript entries: 299102 -including ancestral terms in report. -init GO_DAG Found obo: /usr/local/trinotate/3.1.1/util/../PerlLib/obo/go-basic.obo.gz
I get a ream of errors appearing in the terminal saying the following:
Use of uninitialized value within @x in concatenation (.) or string at /usr/local/trinotate/3.1.1/util/extract_GO_assignments_from_Trinotate_xls.pl line 120, <$fh> line 778.
The error is the same on each line, except for the line number at the end of the error changing. I believe the line that's causing the error is $go_info .= '' . $x[$go_pfam_col];`
In the past I haven't had an issue with this script- it's all run fine. I went back and ran an old annotation file with the script and it worked. The only difference this time is that I have added in custom blast annotations, whereas previously there were none. I'm getting the error with Trinotate v3.0.0 and 3.1.1.
Is it possible that the custom annotations are somehow messing with the script?
Thanks, Charles
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charlesfoster
Hi,
I've successfully generated an annotation file using the Trinotate pipeline. For GO enrichment with GOseq, I wish to create a file with GO annotations mapped to genes. The Trinotate wiki indicates that this can be done with the script extract_GO_assignments_from_Trinotate_xls.pl. As per the instructions, I ran the following:
${TRINOTATE_HOME}/util/extract_GO_assignments_from_Trinotate_xls.pl --Trinotate_xls annotation.xls --G --include_ancestral_terms > go_annotations.txtIt's starts off fine, like so:
Total transcript entries: 299102 -including ancestral terms in report. -init GO_DAG Found obo: /usr/local/trinotate/3.1.1/util/../PerlLib/obo/go-basic.obo.gzI get a ream of errors appearing in the terminal saying the following:
Use of uninitialized value within @x in concatenation (.) or string at /usr/local/trinotate/3.1.1/util/extract_GO_assignments_from_Trinotate_xls.pl line 120, <$fh> line 778.The error is the same on each line, except for the line number at the end of the error changing. I believe the line that's causing the error is
$go_info .= '' . $x[$go_pfam_col];`I end up with a go_annotations.txt file with contents that look OK, I'm just not sure whether it might not be 100% correct because of all the errors.
In the past I haven't had an issue with this script- it's all run fine. I went back and ran an old annotation file with the script and it worked. The only difference this time is that I have added in custom blast annotations, whereas previously there were none. I'm getting the error with Trinotate v3.0.0 and 3.1.1.
Is it possible that the custom annotations are somehow messing with the script?
Thanks, Charles