sqlite3.OperationalError #72
Comments
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Hello, This is indeed very odd... Could you add the following command to the db_loadPresenceAbsence.py right before the line that failed: print tuple(sp) and then run $ db_loadPresenceAbsence.py and let me know what gets printed? Maybe something fishy will come up there that will help me diagnose what happened. As for the effects this has, you should be able to just run the db_loadPresenceAbsence.py (after we fix whatever the problem is) and not have to rerun the whole setup step 2 (loading this is the last step and the rest of the database gets loaded first). You can also still do any analysis you want with the blast results as long as you don't need the presence absence table. |
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Hi, The following is the end of what gets printed: There was so much output that I was not able to capture the first part.
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It looks like something went wrong with parsing a file (most likely the genbank file) here, because a gene sequence and protein sequence got pulled into one of the annotations. I'd recommend looking for this gene in your Genbank files and seeing if anything looks particularly strange for that gene... Regardless, I have pushed up a band-aid for this (makes it not crash if there are tabs in the annotation) so please try to do a git pull and see if it works for you (pull down the latest, then just run db_loadPresenceAbsence.py). As mentioned above the root cause is probably something more insidious -- maybe it wouldn't happen with an updated version of Biopython? If you don't mind missing info on that one gene, the rest of the results look fine up to that point so my guess is this was a very rare occurrence in your dataset and any other analysis that doesn't need to include that gene should be OK. |
I am running ITEP using the 64GB virtual box. The setup_step1 step completed successfully, but running setup_step2 yields the following error:
Traceback (most recent call last):
File "/home/itep/LATEST_ITEP/master/src/internal/db_loadPresenceAbsence.py", line 125, in
cur.execute(cmd, tuple(sp))
sqlite3.OperationalError: table presenceabsence has 24 columns but 36 values were supplied
I think there are 24 columns for "runid", "clusterid", "annote", and 21 genomes. I do not know where 36 values would come from.
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