mattb112885
commented
8 years ago 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.
spaver
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.