Problems with "running annotation script at line 704" and "running run_panoct.pl at line 1174"

[jarrettlebov]

Hi, when I run the command:

perl "$Panoct_bin"/run_pangenome.pl --no_grid --blast_local --panoct_local --use_nuc --working_dir "$Panoct_out" --gb_dir "$Gbks" --panoct_verbose

The following problems are reported:
Problem running annotation script at line 704 Problem with running run_panoct.pl at line 1174

However, a results folder is produced which contains all the outputs I would expect from run_panoct.pl including the matchtables.

I'm not sure if this is something I should be concerned about. Any explanations as to why these problems are being reported would be greatly appreciated. Thanks!

[thclarke]

Good morning. You are correct that the primary output of the pangenome (identification of the core genes, flexible genome islands, etc) have been completed by this stage. The subsequent output are concerning the annotation of the clusters with go terms, anti-microbial resistance, multiple sequence alignment, and more, all through centroid analysis. These steps can be turned off in the beginning by using the "--no-annotation" flag in the command line, or you can ignore them (or run your own analysis on the centroids"), but we have found them very useful. As for what is causing the error, we would need to see further information from the pangenome log files

[jarrettlebov]

Thanks for your reply. I found a problem with some of my gbk files, so I re-ran the panoct pipeline using coding sequence fasta files and attribute files I assembled myself, using the following command:
perl "$Panoct_bin"/run_pangenome.pl -w "$Panoct_out" -g ./genomes.list --no_grid --blast_local --panoct_local --use_nuc --panoct_verbose

Unfortunately, I still get the same problems being reported.

Here is the output from my get_go_annotations.pl.log file:
Problem running hmmer2go 'run': /usr/bin/env perl -I /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/lib /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/bin/hmmer2go run -d /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/data/Pfam-A.hmm -i /local/aberdeen2rw/julie/Jarrett/Ref_genomes/Wolbachia/PanWol/PanOCTpl_out/results/centroids.fasta.cleaned

And here is the output from my hmmer2go.run.pfam.log file:
Can't locate String/RewritePrefix.pm in @INC (you may need to install the String::RewritePrefix module) (@INC contains: /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/lib /usr/local/packages/perl-5.24.0/lib/site_perl/5.24.0/x86_64-linux-thread-multi /usr/local/packages/perl-5.24.0/lib/site_perl/5.24.0 /usr/local/packages/perl-5.24.0/lib/5.24.0/x86_64-linux-thread-multi /usr/local/packages/perl-5.24.0/lib/5.24.0 /usr/local/common/perl/lib .) at /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/lib/App/Cmd/Setup.pm line 77. BEGIN failed--compilation aborted at /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/lib/App/Cmd/Setup.pm line 77. Compilation failed in require at /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/lib/HMMER2GO.pm line 3. BEGIN failed--compilation aborted at /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/lib/HMMER2GO.pm line 3. Compilation failed in require at /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/bin/hmmer2go line 6. BEGIN failed--compilation aborted at /autofs/aberdeen2rw/julie/Jarrett/Programs/PanOCT/PanGenomePipeline-master/pangenome/bin/HMMER2GO/bin/hmmer2go line 6.

Please let me know if there are are log files that would be helpful to provide. I'm a little confused because there is a centroids.fasta in the results output folder which seems to contain annotation information.

Your continued guidance is greatly appreciated.

Thanks, Jarrett

[thclarke]

Good morning- you are sharing the correct log file as far as I can tell. Briefly, it looks like you do not have a necessary perl module (String/RewritePrefix) installed or installed on a path where your perl program can locate it. The quickest way is to just install it with CPAN, but this does require you to have write access to the perl library folder.