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ComparativeGenomicsToolkit / Comparative-Annotation-Toolkit

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AugustusCGP error #244

Open francicco opened 3 years ago

francicco commented 3 years ago

Hi,

Me again. I'm getting this:

ERROR: 2021-02-14 18:13:48,059 - [pid 3967] Worker Worker(salt=024135178, workers=28, host=bc4login2.bc4.acrc.priv, username=tk19812, pid=20263) failed    Task: EvaluateDriverTask for Djun
Traceback (most recent call last):
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/venv/lib/python3.7/site-packages/luigi/worker.py", line 191, in run
    new_deps = self._run_get_new_deps()
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/venv/lib/python3.7/site-packages/luigi/worker.py", line 133, in _run_get_new_deps
    task_gen = self.task.run()
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/cat/__init__.py", line 2083, in run
    results = classify(eval_args)
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/cat/classify.py", line 83, in classify
    ec_df = evaluation_classify(aln_mode, ref_tx_dict, tx_dict, tx_biotype_map, psl_iter, seq_dict)
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/cat/classify.py", line 123, in evaluation_classify
    r.extend(find_indels(tx, psl, aln_mode))
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/cat/classify.py", line 300, in find_indels
    row = parse_indel(left_pos, right_pos, coordinate_fn, tx, q_offset, 'Insertion')
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/cat/classify.py", line 276, in parse_indel
    name=''.join([indel_type, gap_type]))
  File "/mnt/storage/scratch/tk19812/software/Comparative-Annotation-Toolkit/tools/transcripts.py", line 167, in get_bed
    if new_start != exon_intervals[0].start:
IndexError: list index out of range

:( F

francicco commented 3 years ago

Nothing

diekhans commented 3 years ago

Did you get the augustus program built? That is all you need.

diekhans commented 3 years ago

also, check that the date changed on the augustus program, so you are sure it is nbew

francicco commented 3 years ago

I removed it and run make and apparently the Augustus binary is not generated. F

francicco commented 3 years ago

Is there a problem if I use only the augustus binary from your distribution? F

diekhans commented 3 years ago

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.

diekhans commented 3 years ago

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.

francicco commented 3 years ago

I'd use the etraining binary that works... right? F

francicco commented 3 years ago

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