TargetFinder stderr warning observed for some inputs (Galaxy, and externally) when running the targetfinder:1.7--hdfd78af_4 under
- TargetFinder plant small RNA target prediction tool (Galaxy Version 1.7.0), or
- TargetFinder plant small RNA target prediction tool (Galaxy Version 1.7.0+galaxy1)
Some TargetFinder jobs emit this single-line warning in stderr while still producing output:
Use of uninitialized value $offset in substr at /usr/local/bin/targetfinder.pl line 537
Help for scientific users
The practical interpretation is that a job may complete and produce output even when this warning is present. However, outputs from jobs with this stderr warning should be reviewed with caution until the upstream behavior is clarified.
Details:
In the examples observed so far, the stderr message is always this same line. The warning does not appear to be triggered by the current Galaxy wrapper test input (https://usegalaxy.eu/u/jenj/h/test-targetfinder) but private user data can trigger it.
This appears to match the upstream TargetFinder behavior reported here:
Galaxy is using the public BioContainers/CVMFS build:
/cvmfs/singularity.galaxyproject.org/all/targetfinder:1.7--hdfd78af_4
This corresponds to the public Bioconda/BioContainers build:
targetfinder 1.7 hdfd78af_4
The Galaxy wrapper is maintained here:
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/
From the jobs observed so far, the warning seems to be input-specific. It may be related to FASTA label handling and/or hit orientation, but not every reverse-orientation hit triggers it.
TargetFinder stderr warning observed for some inputs (Galaxy, and externally) when running the
targetfinder:1.7--hdfd78af_4underSome TargetFinder jobs emit this single-line warning in stderr while still producing output:
Use of uninitialized value $offset in substr at /usr/local/bin/targetfinder.pl line 537Details:
In the examples observed so far, the stderr message is always this same line. The warning does not appear to be triggered by the current Galaxy wrapper test input (https://usegalaxy.eu/u/jenj/h/test-targetfinder) but private user data can trigger it.
This appears to match the upstream TargetFinder behavior reported here:
Galaxy is using the public BioContainers/CVMFS build:
/cvmfs/singularity.galaxyproject.org/all/targetfinder:1.7--hdfd78af_4This corresponds to the public Bioconda/BioContainers build:
targetfinder 1.7 hdfd78af_4The Galaxy wrapper is maintained here:
https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/From the jobs observed so far, the warning seems to be input-specific. It may be related to FASTA label handling and/or hit orientation, but not every reverse-orientation hit triggers it.