Comments (3)
Hi Alex,
Thanks for using DeepVirFinder.
To help me debug, could you print the input and output of line 212?
print(code)
out = zip(*pool.map(pred, range(0, len(code))))
print(out)
See what you get? Thanks.
Jie
from deepvirfinder.
Hi Jie,
Thanks for the quick reply. After playing around with it some more I actually figured it was due to the length filtering I was putting it. It was too high so none of the contigs were passing through.
Thanks again,
Alex
from deepvirfinder.
If you have a fasta with many small seqs at the end, dvf.py will throw this error. Basically if no sequences pass the size filter in the 100 sequence chunk at the end of the fasta file, the "code" variable will be empty, but pred will still get called. I added an if statement (line 209 in my version) that fixed the issue.
if len(code) >= 1:
print(" processing line "+str(lineNum))
pool = multiprocessing.Pool(core_num)
head, score, pvalue = zip(*pool.map(pred, range(0, len(code))))
from deepvirfinder.
Related Issues (20)
- filelog not imported HOT 3
- Server's running time
- DeepVirFinder gets stuck on some sequences HOT 2
- Runtime Error during test-run HOT 2
- Stuck on loading models? HOT 2
- AttributeError: ('The following error happened while compiling the node', DotModulo(A, s, m, A2, s2, m2), '\n', "module 'numpy.core.multiarray' has no attribute '_get_ndarray_c_version'") HOT 3
- DeepVirFinder isn't work post conda install HOT 1
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- Make a versioned release HOT 2
- File "/data1/qinjunjun/zhu_bingduzu/DeepVirFinder/dvf.py", line 212, in <module>
- Test module falling after installation HOT 4
- Suggestion: Add mkl-service to conda install command HOT 1
- IndexError: list index out of range (by using trained model for viral sequence scanning)
- training.py :: keras - tensorflow version requirements
- hello,I want to know how to set the -l parameter
- problem when running dvf on HPC HOT 2
- [QUESTION] Support Python 3.7 or later HOT 1
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