subprocess.CalledProcessError
liaohu1231 opened this issue · comments
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.
Traceback (most recent call last):
File "run_KnowledgeGraph.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
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