Greetings,
i am currently running a comparative genomics analysis on several genomes (10 to be exact) using protein fasta in OrthoFinder after normalization, the jobs have been running for almost/over two days now with no progress (0 datasets on each) 8 outputs are in yellow and 4 are still queued, if anyone has tried this workflow before and used the orthofinder on protein data, how long does it take on average? I’ve seen several topics here on similar issues and the admins have been clear about how some tools take several days to complete but i just need an estimation for how long this maybe from anyone that has tried it (i am also using the heavier options/parameters for orthofinder because i thought it was a case of leave over night and it will be done by morning, but its not )
i tried to run orthofinder on 2 plant species protein Fastas, and just shortly after launching the job failed (only produced the orthologues tsv file, which is still good but i needed other data too) the error said it reached 10,000 datasets which is a galaxy limit… its my first time doing bioinformatics and discovering usegalaxy platforms, and honestly, can’t understand how the platform has such a limit that would break even the simplest runs on a tool? if i can’t even run orthofinder on two plant species what can that tool be used for? and shouldn’t this be specified on the tool help section especially so users can avoid running bigger jobs which can take up to a week and then fail, i am also running a similar job on 10 plant species on a different history and have been eagerly waiting for the results (its been over 3 days already) and if i knew about the dataset limit and how it would break the job even after a long time, i would have looked elsewhere and not wait around to see it fail (as i am expecting…hope it will survive but i am not sure it will), i strongly recommend adding the warning about the 10,000 datasets (which i didn’t even expect to come out from the analysis) which i assume would face mny plant analysis runs.
Would you like to share more about how this work was set up to run?
The limit inside of orthofinder is specific to the tool, and it is with respect to the number of temporary working files created, not dataset files, correct? I’m pretty sure this would be a limit no matter where the original algorithm was run: inside of Galaxy or anywhere else. The warning is likely indicating either a missing data preparation step or that there is potentially a parameter tuning issue to address.
However I may be misunderstanding! We can confirm!
As a reference, the protocol is from this source and would be the best resource to follow as we work through this.
The current computational resource allocation at UseGalaxy servers is this.
Please let us know if you would like more help! I think others had trouble helping because the job inputs, logs, and full error messages were not shared. You can do that now for some feedback! If you would rather share in a direct message, please let me know and I can start one up.
