phyluce_probe_run_multiple_lastzs_sqlite v1.7 issues

[michaelforthman]

Hi Brant,

I've been having trouble getting the phyluce_probe_run_multiple_lastzs_sqlite utility to run on 1.7.0 and 1.7.1.

For 1.7.0, I specify an output directory to be created when running the job, but it never creates the folder and terminates because it cannot locate it. If I re-run the job after manually created it on UF's cloud-computer, it terminates because the output directory already exists.

For 1.7.1, there seems to be some issue with sqlite, but I'm not sure what is causing the problem (neither does our cloud-computing staff):

Traceback (most recent call last):

File "/apps/phyluce/1.7.1/bin/phyluce_probe_run_multiple_lastzs_sqlite", line 297, in

main()

File "/apps/phyluce/1.7.1/bin/phyluce_probe_run_multiple_lastzs_sqlite", line 286, in main

align_against_scaffolds(log, cur, args, path)

File "/apps/phyluce/1.7.1/bin/phyluce_probe_run_multiple_lastzs_sqlite", line 225, in align_against_scaffolds

create_species_lastz_tables(cur, g)

File "/apps/phyluce/1.7.1/bin/phyluce_probe_run_multiple_lastzs_sqlite", line 148, in create_species_lastz_tables

cur.execute(query)

sqlite3.OperationalError: near "-": syntax error

Cheers, Michael

[brantfaircloth]

Looks like in 1.7.1 there may be a hyphen in your taxon names?

[michaelforthman]

Thanks, that was the issue!