Prodigal Gene Predictor: error option (# Other genetic codes 1-25) stderr Invalid translation table specified

tvtv195 · August 26, 2026, 4:27pm

I am experiencing a bug in this specific version of the Galaxy wrapper (Galaxy Version 2.6.3+galaxy0).

The developer forgot to link the conditional text field container to the # : Other genetic codes 1-25 selection choice. Because that field is missing from the interface, the underlying code tries to execute a broken command line (prodigal -g), which immediately causes my job to fail.

jennaj · September 7, 2026, 5:55pm

Welcome @tvtv195

Thanks for reporting the issue! I was able to reproduce the problem and get it reported. Please feel free to add more details to the ticket if I missing anything. If I misunderstood anything, please also let me know here and we can discuss it more. I tested a matrix however this didn’t include all combinations of parameters.

Request: supply missing reference for Prodigal (re: # Other genetic codes 1-25) · Issue #1707 · galaxyproject/usegalaxy-tools · GitHub

My initial suspicion is that the # character is not parsed correctly when constructing the command string. I remember this coming up before but I don’t think the discussion was here at the forum, so I am glad you asked!

I’m going to annotate this topic so others who run into the same problem can find it. (it will appear “resolved” but this is only to show the topic at the bottom of tool forms, we will know that this is still an open issue based on the other tags). Please feel free to keep commenting here!

Our apologies for the delay in tracking this! Next time, if you share the job error, more moderators will be able to help you quicker!

Full details in the issue ticket above but these are a few highlights below to aid with searches.

Parameters

github.com/galaxyproject/tools-iuc

tools/prodigal/prodigal.xml

7afd887ff


      
          <param type="select" name="trans_table" label="Specify a translation table to use" help="-g" >
              <option value="11">11 : Standard Bacteria/Archaea (default)</option>
              <option value="4">4 : Mycoplasma/Spiroplasma</option>
              <option value="#"># : Other genetic codes 1-25</option>

Works
'(single|meta)' -g '(4|11)'

prodigal -i '/corral4/main/objects/d/f/8/dataset_df8732da-6c1b-455e-b08f-fd9a942dfcbd.dat' -o '/corral4/main/jobs/079/596/79596942/outputs/dataset_30ca3796-c448-4727-8e40-fcdf7bb2db7e.dat' -f 'gbk' -p 'meta' -g '4' -a '/corral4/main/jobs/079/596/79596942/outputs/dataset_826c0b17-2c17-41f6-9a3b-a3668ded23a9.dat' -d '/corral4/main/jobs/079/596/79596942/outputs/dataset_8acb0560-c846-423f-a0a4-23333ba8a8d9.dat' -s '/corral4/main/jobs/079/596/79596942/outputs/dataset_46c7aef7-fcb7-472c-bfe5-e0312275b74b.dat'

Fails
'(single|meta)' -g '__pd__'

prodigal -i '/data/dnb13/galaxy_db/files/8/a/0/dataset_8a0d4664-770a-4625-b031-66263efe468d.dat' -o '/data/jwd06/main/000/112/243/112243092/outputs/dataset_0d8f7b21-035c-4d54-94d9-ec19e0288037.dat' -f 'gbk' -p 'single' -g '__pd__' -a '/data/jwd06/main/000/112/243/112243092/outputs/dataset_7a611c84-9814-42e1-86e5-f22274f1ef89.dat' -d '/data/jwd06/main/000/112/243/112243092/outputs/dataset_5ae996e4-cc56-4280-a6fa-113a99f09abb.dat' -s '/data/jwd06/main/000/112/243/112243092/outputs/dataset_8d808962-0f31-44f0-ad33-88ed3155973a.dat'

Tool Standard Error will include
Invalid translation table specified.

and look like this:

Compare to original command strings here

Advice By Input Type · hyattpd/Prodigal Wiki · GitHub