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They come from an assembled transcriptome/ORFs called by transdecoder.
I am getting the following error:
Multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/apps/python3/3.7.0/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/apps/python3/3.7.0/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/00_scripts/py3-venv/lib/python3.7/site-packages/pandarallel/pandarallel.py", line 64, in global_worker
return _func(x)
File "/home/00_scripts/py3-venv/lib/python3.7/site-packages/pandarallel/pandarallel.py", line 116, in wrapper
**kwargs
File "/home/00_scripts/py3-venv/lib/python3.7/site-packages/pandarallel/data_types/series.py", line 20, in worker
return series.apply(func, *args, **kwargs)
File "/home/00_scripts/py3-venv/lib/python3.7/site-packages/pandas/core/series.py", line 3848, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File "pandas/_libs/lib.pyx", line 2327, in pandas._libs.lib.map_infer
File "razor.py", line 139, in <lambda>
df['Analysis_'] = df['Sequence'].parallel_apply(lambda x: razor_predict(x, m))
File "razor.py", line 71, in razor_predict
newObj = detector.RAZOR(seq=seq, max_scan=max_scan)
File "/scratch/user/razor/Razor/libs/detector.py", line 31, in __init__
self.seq = functions.validate(seq, self.max_scan)
File "/scratch/user/razor/Razor/libs/functions.py", line 77, in validate
"Unknown residues in the input "
ValueError: Unknown residues in the input sequence.
Only standard amino acid codes are allowed.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "razor.py", line 159, in <module>
main()
File "razor.py", line 139, in main
df['Analysis_'] = df['Sequence'].parallel_apply(lambda x: razor_predict(x, m))
File "/home/00_scripts/py3-venv/lib/python3.7/site-packages/pandarallel/pandarallel.py", line 462, in closure
map_result,
File "/home/00_scripts/py3-venv/lib/python3.7/site-packages/pandarallel/pandarallel.py", line 396, in get_workers_result
results = map_result.get()
File "/apps/python3/3.7.0/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
ValueError: Unknown residues in the input sequence.
Only standard amino acid codes are allowed.
I tried to run a check using seqkit seq -v -V proteins.fasta, but that doesn't find the culprit residue. Do you have any other idea what I could try?
The text was updated successfully, but these errors were encountered:
The problem is because of the Unknown residues in the input sequence. We've pushed a fix (aa63c3a).
By default, we check for non standard residues within the first 95 residues. If your sequence has unknown residues within first 95 residues, you can use the parameter -m to reduce the maximum length to check/scan.
Hi,
I am running
razor
on my proteins as:They come from an assembled transcriptome/ORFs called by transdecoder.
I am getting the following error:
I tried to run a check using
seqkit seq -v -V proteins.fasta
, but that doesn't find the culprit residue. Do you have any other idea what I could try?The text was updated successfully, but these errors were encountered: