linnabrown
commented
5 years ago Hi, thanks for your feedback and sorry for my late response cause I am going abroad recently.
About this problem, it has the same reason with this case(https://github.com/linnabrown/run_dbcan/issues/13#issuecomment-523047958).
Please refer my answer to another user.
I recommend you to use dokcer to keep away from this problem.
Thanks for using! 🍡
Le
dbcan=/mnt/lustre/user/wubin/01.Program/Scripts/02.software/run_dbcan/run_dbcan.py fa=/mnt/lustre/user/wubin/02.Projects/MetaGenome/02.MetaGenome/01.Stool/06.funcAnno/03.CAZy/test.fa outdir=/mnt/lustre/user/wubin/02.Projects/MetaGenome/02.MetaGenome/01.Stool/06.funcAnno/03.CAZy/test dbdir=/mnt/lustre/user/wubin/01.Program/Scripts/03.data/metaGenome/funcAnno/CAZyme
python $dbcan $fa protein --out_dir $outdir --db_dir $dbdir -t hmmer
=================================================================== the error was like this:
===================================================================
*2. HMMER start***
*2. HMMER end***** python: can't open file 'hmmscan-parser.py': [Errno 2] No such file or directory Waiting on signalP SignalP complete Preparing overview table from hmmer, hotpep and diamond output... Traceback (most recent call last): File "/mnt/lustre/user/wubin/01.Program/Scripts/02.software/run_dbcan/run_dbcan.py", line 553, in
for i in range(1,len(arr_hotpep)):
NameError: name 'arr_hotpep' is not defined
I have to add the absolute path of "hmmscan-parser.py" in run_dbcan.py which is "/mnt/lustre/user/wubin/01.Program/Scripts/02.software/run_dbcan/hmmscan-parser.py"
and then run "python $dbcan $fa protein --out_dir $outdir --db_dir $dbdir -t hmmer" again.
I still got the error:
*2. HMMER start***
*2. HMMER end***** Waiting on signalP SignalP complete Preparing overview table from hmmer, hotpep and diamond output... Traceback (most recent call last): File "/mnt/lustre/user/wubin/01.Program/Scripts/02.software/run_dbcan/run_dbcan.py", line 553, in
for i in range(1,len(arr_hotpep)):
NameError: name 'arr_hotpep' is not defined
the Hotpep directory are in the same directory as run_dbcan.py
$ls /mnt/lustre/user/wubin/01.Program/Scripts/02.software/run_dbcan CGCFinder.py EscheriaColiK12MG1655.faa EscheriaColiK12MG1655.gff Hotpep log run_dbcan_backup.py tools Dockerfile EscheriaColiK12MG1655.fna hmmscan-parser.py input.fas README.md run_dbcan.py
then I have 2 questions: