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KennthShang / PhaGCN2.0

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subprocess.CalledProcessError #6

Open liaohu1231 opened 9 months ago

liaohu1231 commented 9 months ago

Running Diamond... Knowledge Graph Error for file contig_0 Traceback (most recent call last): File "/public3/home/sc52870/soft/PhaGCN2.0/run_Speed_up.py", line 129, in out = subprocess.check_call(cmd, shell=True) File "/public3/home/sc52870/miniconda3/envs/phagcn2/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'cat pred/* > phage10_final_prediction.csv' returned non-zero exit status 1. diamond v0.9.14.115 | by Benjamin Buchfink buchfink@gmail.com Licensed under the GNU AGPL https://www.gnu.org/licenses/agpl.txt Check http://github.com/bbuchfink/diamond for updates.

liaohu1231 commented 9 months ago

Traceback (most recent call last): File "runKnowledgeGraph.py", line 129, in = subprocess.check_call("cat {0} > {1}".format(file_out_fn+"", all_protein_f), shell=True) File "/public3/home/sc52870/miniconda3/envs/phagcn2/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'cat all_proteins/ > out/all_translate_proteins.fa' returned non-zero exit status 1. Knowledge Graph Error for file contig_0 cat: pred/*: No such file or directory

yuanwenguang666 commented 2 months ago

Sorry for the slow response.

From your logs, it seems that there are too few matching sequences in your prediction data. I recommend that you test to see if your sequences length is > 1700bp or have no gaps, or use more sequences to test.

Thank you for your question. WenGuang