Open mvdbeek opened 1 year ago
Thanks for the compilation. For the future we should check planemo before releases or planemo PR branches against IUC.
galaxy.jobs.runners ERROR 2022-11-28 14:54:24,341 [pN:main.1,p:3063045,tN:LocalRunner.work_thread-0] (12/3064188) Job wrapper finish method failed
Traceback (most recent call last):
File "/tmp/tmpiyzvjhew/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 628, in _finish_or_resubmit_job
job_wrapper.finish(
File "/tmp/tmpiyzvjhew/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1850, in finish
self._finish_dataset(output_name, dataset, job, context, final_job_state, remote_metadata_directory)
File "/tmp/tmpiyzvjhew/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1668, in _finish_dataset
dataset.datatype.set_meta(dataset, overwrite=False)
File "/tmp/tmpiyzvjhew/galaxy-dev/lib/galaxy/datatypes/goldenpath.py", line 28, in set_meta
AGPFile(dataset.file_name)
File "/tmp/tmpiyzvjhew/galaxy-dev/lib/galaxy/datatypes/goldenpath.py", line 137, in __init__
self._read_file()
File "/tmp/tmpiyzvjhew/galaxy-dev/lib/galaxy/datatypes/goldenpath.py", line 174, in _read_file
raise AGPError(self.fname, line_number, "detected more than 9 tab delimited fields")
galaxy.datatypes.goldenpath.AGPError:
FILE: /tmp/tmpiyzvjhew/files/000/dataset_15.dat
LINE: 1
ERROR: detected more than 9 tab delimited fields
This https://github.com/galaxyproject/tools-iuc/pull/4984 might be another case. The tests are successful if executed with planemo 0.74 and fail with 0.75. No idea why .. but at least 0.75 is correct :)
clair3
fails for the same reason. It tries to get a file phased_bam.bam
from the workdir which is absent. Then setting metadata fails:
setting metadata externally failed for HistoryDatasetAssociation 15: Traceback (most recent call last):
File "/tmp/tmp1mff07rd/galaxy-dev/lib/galaxy/metadata/set_metadata.py", line 425, in set_metadata_portable
set_meta(dataset, file_dict)
File "/tmp/tmp1mff07rd/galaxy-dev/lib/galaxy/metadata/set_metadata.py", line 180, in set_meta
set_meta_with_tool_provided(
File "/tmp/tmp1mff07rd/galaxy-dev/lib/galaxy/metadata/set_metadata.py", line 118, in set_meta_with_tool_provided
dataset_instance.datatype.set_meta(dataset_instance, **set_meta_kwds)
File "/tmp/tmp1mff07rd/galaxy-dev/lib/galaxy/datatypes/binary.py", line 746, in set_meta
pysam.index(dataset.file_name, index_file.file_name)
File "/home/berntm/.planemo/gx_venv_3/lib/python3.9/site-packages/pysam/utils.py", line 69, in __call__
raise SamtoolsError(
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools index: "/tmp/tmp1mff07rd/job_working_directory/000/9/outputs/galaxy_dataset_88447f80-d7e1-4ecd-ac6d-91c3586faa20.dat" is in a format that cannot be usefully indexed\n'
We got about 200 of those now, which isn't great. For the most part these are bugs in Galaxy or planemo, but let's track this here for now.