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This logging means that this line:
https://github.com/DataBiosphere/toil/blob/master/src/toil/batchSystems/lsf.py#L122
is not being parsed correctly by lsf.py batch system.
however, it still works because default return value from that function is return None which is the same as return value for when job is running
return None
however we need to fix this debug logging as it should be printing "bjobs detected job started but not completed: <job id>".
"bjobs detected job started but not completed: <job id>"
DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221600 DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221601 DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221601 DEBUG:toil.batchSystems.abstractGridEngineBatchSystem:No activity, sleeping for 1s DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221600 DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221600 DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221601 DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221601 DEBUG:toil.batchSystems.abstractGridEngineBatchSystem:No activity, sleeping for 1s DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221600 DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221600 DEBUG:toil.batchSystems.lsf:Checking job exit code for job via bjobs: 16221601 DEBUG:toil.batchSystems.lsf:bjobs detected job pending for job: 16221601 DEBUG:toil.batchSystems.abstractGridEngineBatchSystem:No activity, sleeping for 1s
The text was updated successfully, but these errors were encountered:
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This logging means that this line:
https://github.com/DataBiosphere/toil/blob/master/src/toil/batchSystems/lsf.py#L122
is not being parsed correctly by lsf.py batch system.
however, it still works because default return value from that function is
return None
which is the same as return value for when job is runninghowever we need to fix this debug logging as it should be printing
"bjobs detected job started but not completed: <job id>"
.The text was updated successfully, but these errors were encountered: