If transMap does not produce any projections, this error occurs in filter_transmap.py:
ERROR: 2021-01-10 21:04:02,374 - [pid 23388] Worker Worker(salt=987820952, workers=5, host=marina-cat-hprc-chry-all-6hxxq, username=root, pid=6624) failed Task: FilterTransMap for HG01123.pat
Traceback (most recent call last):
File "/Comparative-Annotation-Toolkit/cat_env/lib/python3.7/site-packages/luigi/worker.py", line 191, in run
new_deps = self._run_get_new_deps()
File "/Comparative-Annotation-Toolkit/cat_env/lib/python3.7/site-packages/luigi/worker.py", line 133, in _run_get_new_deps
task_gen = self.task.run()
File "/Comparative-Annotation-Toolkit/cat/init.py", line 1293, in run
json_target)
File "/Comparative-Annotation-Toolkit/cat/filter_transmap.py", line 207, in filter_transmap
resolved_df = combined_tx_df.merge(merged_df, on='GeneId', how='left')
File "/Comparative-Annotation-Toolkit/cat_env/lib/python3.7/site-packages/pandas/core/frame.py", line 7963, in merge
validate=validate,
File "/Comparative-Annotation-Toolkit/cat_env/lib/python3.7/site-packages/pandas/core/reshape/merge.py", line 87, in merge
validate=validate,
File "/Comparative-Annotation-Toolkit/cat_env/lib/python3.7/site-packages/pandas/core/reshape/merge.py", line 656, in init
self._maybe_coerce_merge_keys()
File "/Comparative-Annotation-Toolkit/cat_env/lib/python3.7/site-packages/pandas/core/reshape/merge.py", line 1165, in _maybe_coerce_merge_keys
raise ValueError(msg)
ValueError: You are trying to merge on float64 and object columns. If you wish to proceed you should use pd.concat
The transMap files in the work directory for the genome in question are empty.
This was observed when trying to annotate human chrM genomes, as well as one chrY genome. The pipeline exits without producing any annotations (output directory is empty except for databases/*.db).
CAT should check for empty transMap files, and if files are empty, exit with an error message and output appropriate empty downstream files. CAT should then finish annotating other genomes. The user should be warned (in a noticeable way) that this error happened.
If transMap does not produce any projections, this error occurs in filter_transmap.py:
The transMap files in the work directory for the genome in question are empty.
This was observed when trying to annotate human chrM genomes, as well as one chrY genome. The pipeline exits without producing any annotations (output directory is empty except for
databases/*.db).CAT should check for empty transMap files, and if files are empty, exit with an error message and output appropriate empty downstream files. CAT should then finish annotating other genomes. The user should be warned (in a noticeable way) that this error happened.