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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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No such column error in phyluce_assembly_get_fastas_from_match_counts #320

Open louisfnastasi opened 8 months ago

louisfnastasi commented 8 months ago

I've received the below error while running phyluce_assembly_get_fastas_from_match_counts with the following script:

phyluce_assembly_get_fastas_from_match_counts \
    --contigs /storage/group/hmh19/default/UCEs_working/assemblies/assemblies-to-run \
    --locus-db /storage/group/hmh19/default/UCEs_working/assembly-uce-search-results/probe.matches.sqlite \
    --match-count-output /storage/group/hmh19/default/UCEs_working/taxon-sets/all/all-taxa-incomplete-with-hearn.conf \
    --output all-taxa-incomplete-with-hearn.fasta \
    --incomplete-matrix all-taxa-incomplete-with-hearn.incomplete \
    --log-path log
image

Any ideas as to what the error is the result of? I checked the files output by the previous stem including the .conf listed in match-count-output and Aulacidea tavakolii is present there (as well as previous steps in the process) - everything looks normal.

brantfaircloth commented 8 months ago

Hard to say without more information (like the output from match_contigs_to_probes). The error indicates that the column is not present in the database - so you could take a look at the tables in the database to see if the column is really present (I’m guessing it is not) or if there is some error with the column name.