nextgenusfs
commented
6 years ago Well certainly a pasa issue.... what it is trying to do here is not re-run PASA alignment step if it doesn't have to, so it looks into the DB to see if it has been run already, since it seems to think it has been run before, then it skips that step and tries to run PASA comparison (or update gene models).
If you ran PASA previously using a different --species name this might be the issue. It is setup so that if you run funannotate train followed by funanntoate predict and then finally add UTRs with funannotate update that it will re-use the PASA config file located in the training subfolder. To bypass this, say perhaps PASA failed and you ran it with another config file successfully, you can pass that config file to funannotate update --pasa_config.
So likely what is happening is that there is a pasa config file in the training directory that is causing the error. So you can 1) delete it and it will re-run alignment step, or 2) pass the script the correct pasa_config file used to run PASA the first time.
AnotherSimon
peterthorpe5![https://github.githubassets.com/images/email/message_cards/header.png","avatar_image_url":"https://github.githubassets.com/images/email/message_cards/avatar.png","action":{"name":"Open](https://github.githubassets.com/images/email/message_cards/header.png","avatar_image_url":"https://github.githubassets.com/images/email/message_cards/avatar.png","action":{"name":"Open){kind=link}
According to the manual, after running gene prediction (with RNAseq support), one should run update "to add UTR data to the predictions and fix gene models". When running:
funannotate update -i MyOrganismThe process seems to start off alright but soon fails:
Relevant logging info was found in funannotate-update.log:
Manually connecting to the mysql instance confirms that this table does not exist for db "My_bug_strainNum". Prediction step did not raise any errors or highly visible warnings.
PS: This may or may not be relevant but the first time running predict it failed because I needed to add the hooks to
@INCas follows:My_bug_strainNum was manually dropped and prediction rerun.