There seems to be confusion between the input sample name and the output folder names that are used in MetaPathways partciularly when doing basting on the grid.
Here we specified an exact .fasta file instead of just an input directory. The output directory was also a little ambiguous (but this is something normal people are going to do). This caused a float division error when it got to the grid. We have to think of an elegant want to get around this if the user doesn't specify an exact directory or we have to make it clear that when you specify an exact input file we also expect an exact output directory (not creating a new subdirectory).
The Original Command:
ariahahn@showgirl:~/Desktop/MetaPathways $ metapathways.py -i input/Fosmid_Ends_WL_Jan17/LTSP_ends.fasta -o output -p template_param.txt -v -r overlay
True True
WARNING: Refseq BLAST output output/blast_results//LTSP_ends.refseq.blastout not found!
Will have to Skip taxonomic information in annotation table :(
**********************************************************
******************** Running metapaths *******************
**********************************************************
input/Fosmid_Ends_WL_Jan17/LTSP_ends.fasta
**********************************************************
The Error:
Issuing Command : {'run_type': 'overlay', 'dbnames': ['metacyc'], 'sample_name': 'output', 'max_parallel_jobs': '400', 'server': 'bugaboo.westgrid.ca', 'database_files': ['metacyc-v4-2011-07-03'], 'batch_size': '200', 'user': 'ahahn'}
6. Blasting ORFs against reference database - metacyc-v4-2011-07-03 ....
Server bugaboo.westgrid.ca is working
Successfully copied daemon script
'MetaPathways'
found
'MetaPathways/databases'
found
'MetaPathways/executables'
found
MetaPathways/executables/blastp
found
MetaPathways/executables/formatdb
found
MetaPathways/databases/metacyc-v4-2011-07-03
found
already formatted
Sample folder output
NOT found
created!
MetaPathways/output/.qstatdir
NOT found
created!
MetaPathways/output/output.qced.faa
NOT found
copied
Number of sequence files created :0
[ Traceback (most recent call last): ]
File "./metapathways.py", line 233, in <module>
main(sys.argv[1:])
File "./metapathways.py", line 228, in main
run_type = run_type
File "/Users/ariahahn/Desktop/MetaPathways/libs/python_modules/metapaths.py", line 1187, in run_metapathways
command_handler(commands, status_update_callback, logger, stepslogger, command_line_params)
File "/Users/ariahahn/Desktop/MetaPathways/libs/python_modules/metapaths_pipeline.py", line 147, in call_commands_serially
blastgrid(c[1])
File "/Users/ariahahn/Desktop/MetaPathways/libs/python_modules/BlastGrid.py", line 528, in blastgrid
current = int((completedsamples*100)/numsamples)
ZeroDivisionError: float division
We also noticed that there was an "output" directory on westgrid where we expected a sample name directory because it got confused between directory and sample name.
There seems to be confusion between the input sample name and the output folder names that are used in MetaPathways partciularly when doing basting on the grid.
Here we specified an exact .fasta file instead of just an input directory. The output directory was also a little ambiguous (but this is something normal people are going to do). This caused a float division error when it got to the grid. We have to think of an elegant want to get around this if the user doesn't specify an exact directory or we have to make it clear that when you specify an exact input file we also expect an exact output directory (not creating a new subdirectory).
The Original Command:
The Error:
We also noticed that there was an "output" directory on westgrid where we expected a sample name directory because it got confused between directory and sample name.