Open francicco opened 3 years ago
Nothing
Did you get the augustus program built? That is all you need.
also, check that the date changed on the augustus program, so you are sure it is nbew
I removed it and run make and apparently the Augustus binary is not generated. F
Is there a problem if I use only the augustus binary from your distribution? F
on the official https://github.com/Gaius-Augustus/Augustus
master branch git pull make clean make -k MYSQL=false >&make.out
It may fail so some the minor programs like bam2hints , but if it doesn't build the augustus program, attach make.out to the ticket.
You should not have a problem the program built from my fork with the other programs, however this will not help solve your problem with long genes.
I'd use the etraining binary that works... right? F
Ok guys...
Now I'm getting this:
ERROR: 2021-03-29 20:13:46,080 - [pid 116231] Worker Worker(salt=880016249, workers=64, host=bp1-compute00194.data.bp.acrc.priv, username=tk19812, pid=113305) failed Task: FilterTransMap for Mcin
Traceback (most recent call last):
File "/work/tk19812/software/Comparative-Annotation-Toolkit/venv/lib/python3.8/site-packages/luigi/worker.py", line 191, in run
new_deps = self._run_get_new_deps()
File "/work/tk19812/software/Comparative-Annotation-Toolkit/venv/lib/python3.8/site-packages/luigi/worker.py", line 133, in _run_get_new_deps
task_gen = self.task.run()
File "/work/tk19812/software/Comparative-Annotation-Toolkit/cat/__init__.py", line 1290, in run
resolved_df = filter_transmap(tm_args.tm_psl, tm_args.ref_psl, tm_args.tm_gp,
File "/work/tk19812/software/Comparative-Annotation-Toolkit/cat/filter_transmap.py", line 164, in filter_transmap
noncoding_merged_df, noncoding_collapse_filtered = filter_clusters(noncoding_clustered, transcript_gene_map,
File "/work/tk19812/software/Comparative-Annotation-Toolkit/cat/filter_transmap.py", line 352, in filter_clusters
collapsed_df = pd.DataFrame(collapsed_genes, columns=['GeneId', 'CollapsedGeneIds', 'CollapsedGeneNames'])
File "/work/tk19812/software/Comparative-Annotation-Toolkit/venv/lib/python3.8/site-packages/pandas/core/frame.py", line 490, in __init__
mgr = init_dict({}, index, columns, dtype=dtype)
File "/work/tk19812/software/Comparative-Annotation-Toolkit/venv/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 239, in init_dict
val = construct_1d_arraylike_from_scalar(np.nan, len(index), nan_dtype)
File "/work/tk19812/software/Comparative-Annotation-Toolkit/venv/lib/python3.8/site-packages/pandas/core/dtypes/cast.py", line 1449, in construct_1d_arraylike_from_scalar
dtype = dtype.dtype
AttributeError: type object 'object' has no attribute 'dtype'
INFO: 2021-03-29 20:13:46,415 - Informed scheduler that task FilterTransMap_False_True_True_5f5e0901b6 has status FAILED
Cheers F
Hi,
Me again. I'm getting this:
:( F