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carringtonlab / p-sams

The Plant Small RNA Maker Suite
MIT License
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"TargetFinder": No results for amiRNA0, with tomato (Solanum lycopersicum) annotation ITAG4.0 #2

Open javijevi opened 3 years ago

javijevi commented 3 years ago

I'm trying to use psams.pl -c amiRNA with tomato transcripts (versión ITAG4.0), and have no errors (just warnings), but the result has no results for TargetFinder, showing the following in the JSON results file:

  "TargetFinder": No results for amiRNA0

When seeing the process running, I cannot see (as with Arabidopsis) the ssearch35_t running.

Please find attached the STDERR, the JSON result file, and the TargetFinder log obtained with DEBUG => 1.

I have p-sams running fine with other species.

Could be the ID of the transcripts an issue? In tomato they are, for example, Solyc12g100320.2.1 (observe that the locus name contains a dot, and the transcript number is indicated by the second dot).

Thanks in advance and best regards,

Javier. stderr.log stdout.json.txt targetfinder.log

javijevi commented 3 years ago

I've found the solution, although I cannot understand it:

For any reason, TargetFinder/ssearch35_t doesn't like the transcripts filename used and set in psams.conf file. It was slycopersicum4.4.transcripts.fasta. When moved to just transcripts.fasta (and changed accordingly in the psams.conf file), it runs fine.