nextgenusfs
commented
6 months ago It seems that tbl2asn failed in the update step (which creates the genbank file from the tbl annotation file). From what you have here, I can't see why it would have failed, especially if it worked in the predict step as you suggested.
When you passed this to annotate, -i $OUTDIR/$BASE, is that this folder (annotate/Histoplasma_capsulatum_1371NJ)?
The script is indeed dying because there is no genbank file, although perhaps this shouldn't be a hard stop. The scripts could generate the necessary output in a different way (and maybe it should).
Ideally you'd like to figure out why tbl2asn failed, you could run that step manually and see if you get an error. Alternative work around is just to run annotate with the FASTA + GFF3 files from update and provide a new output directory, this will regenerate the files it needs and will not rely on the genbank input.
tania-k
hyphaltip
Funannotate version = funannotate v1.8.16
Hello Funannotate folks, Thanks for producing a wonderful program! I am currently experiencing an issue that I am unsure how to solve. I have progressed through the steps in Funannotate, using mask, train, predict, update, antismash, and iprscan, and am now in the final annotate step but I am receiving an issue running it.
The way I am running the script is: With a lot of variables.
The error appears as Histoplasma_capsulatum_1371NJ
As I look through my other runs, I noticed that my update step ran just fine in the log files, but it did not produce all the files it usually does (specifically gbk file). I understand that to run this step it would be pulling from the update_results folder. I had the antismash step run pull from the predict_results folder instead as the gbk file was not produced, but I want to understand why, and make sure the 5' and 3' UTRs are detected here by re-running my analysis.
The GBK file is empty while the rest of my files are there. Looking at my update log file.
The more verbose logfile looks like.
Any suggestions of where else to look, or if I am missing something, please let me know.
Thank you for your time.