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brinkmanlab / IslandCompare

Pipeline for detecting and annotating genomic islands and relationships between the respective genomes
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BioPhylo Parse Tree order not setting failure state #164

Closed innovate-invent closed 5 years ago

innovate-invent commented 5 years ago

This exception doesn't cause the tool to fail.

Traceback (most recent call last):
  File "/project/6004808/ncm3/galaxy-19.05/galaxy-tool-dependencies/_conda/envs/mulled-v1-753eca0881a7204c1d96184412e9982583d6ee338658ce913c62debd6f9c70ca/lib/python3.7/site-packages/Bio/Phylo/_io.py", line 63, in read
    tree = next(tree_gen)
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 2, in <module>
  File "/project/6004808/ncm3/galaxy-19.05/galaxy-tool-dependencies/_conda/envs/mulled-v1-753eca0881a7204c1d96184412e9982583d6ee338658ce913c62debd6f9c70ca/lib/python3.7/site-packages/Bio/Phylo/_io.py", line 65, in read
    raise ValueError("There are no trees in this file.")
ValueError: There are no trees in this file.
innovate-invent commented 5 years ago

This can be attributed to a misconfigured galaxy job_conf infinitely rescheduling the job. This has been fixed.