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Description
Hi Jon,
Thank you for coming out with this great tool. I have run into several problems when trying to use funannotate2-addons.
For the four main pipelines: emapper, iprscan, signalp6 and antismash, only emapper works as expected and the output could be successfully merge with funanntoate2 annotate. iprscan produces this results:
[Sep 18 09:22 AM] Python v3.10.18; funannotate2-addons v25.8.4
[Sep 18 09:22 AM] Redirecting InterProScan output to 2.Predict/annotate_misc/iprscan.iprscan.log
[Sep 18 09:23 AM] InterProScan output file not found: 2.Predict/annotate_misc/iprscan.xml
[Sep 18 09:23 AM] Failed to run InterProScan
I managed to parsed manually with the output looks similar to that of emapper's with 3 columns, etc. However, the output cannot be merged with the rest in the annotate step using either --curated-names or -a. Same issue with signalp6.
My question is: Can funanntoate2 annotate takes multiple *.txt file from emapper, iprscan, signalp6 and antismash; or does it only take one file after all of the four *.txt files are merged into one?
I tried to manipulate the output file from emapper by specifying go_terms in the middle column and use a GO:XXXX in the third. This did not add the GO term to the annotate file as well.
Thanks for your help!