Errors using Maker in Galaxy Europe

Dear Galaxy team,

I have been trying to annotate a sequence and I am in the middle of Maker .It doesnt get finished and a message is coming to contact Galaxy team.
Can anyone kindly help me to fix this.

Best regards,
Jagath Ranasinghe

I may be having a similar issue on Galaxy Europe. My second Maker run just “finished” and the jobs are green, but they have 0 lines. The error message doesn’t appear to say anything specific (aside from the ever-present “@2” interpolation issue). It just lists all the widgets it ran, etc. I shouldn’t have any reason for an error, because the first round worked well. The only change for the second round were the Augustus and SNAP predictors, but they were properly generated without problems.

But I didn’t get the error notice or the message to contact the Galaxy team.

I would have liked to troubleshoot before restarting the job – especially since this job took a whole month on 12 cores – but I don’t see anything to troubleshoot.

If anyone from Galaxy knows what’s going on, please let us know.

My job ended prematurely again. This time I got the error message

MAKER WARNING: The file dataset_57059cd3-60c8-42c5-934d-d85d45a09f19.maker.output/dataset_57059cd3-60c8-42c5-934d-d85d45a09f19_datastore/22/44/#####//theVoid.#####/#####.abinit_masked.0.local.augustus
did not finish on the last run and must be erased
examining contents of the fasta file and run log

at the end of each attempt. And then it simply said Maker is finished, instead of first saying

Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output

like normal. So I now wonder if this is an Augustus problem. I thought I’d post this update in case anyone else is having this error, or if anyone has ideas of what’s wrong. For now I’m going to retrain Augustus and SNAP.

Dear Jared,
Thank you very much for the mail.I also got the same issue and I wrote it to the Galaxy team.Probably I feel that there is an issue with Augustus.SNAP is working and main issue with Augustus.If I find any solution I will let you know.

Best regards,
Jagath Ranasinghe

1 Like

Thanks, @Jagath_Ranasinghe.

Quick update: my retrained Augustus file size is almost 3 times larger than the one I made a month ago (~660 kb vs ~230 kb). I just restarted my Maker run; hopefully the problem will be fixed.

Update: 2 of my jobs ended in an error again after 9 and 21 days, but this time with no tool error message. There was only this in the red box:

tool error
An error occurred with this dataset:
Cluster could not complete job

I suppose I’ll restart it. If anyone has any suggestions, let me know.