Error in DIAMOND_specific_organism_retriever.py

[Indah Oktaviani]

Hi, Sam. 

I've been running agregation step in samsa2 and want to run  DIAMOND_specific_organism_retriever.py but I meet this error message:

Database is read and set up, moving on to the infile...
Traceback (most recent call last):
  File "DIAMOND_specific_organism_retriever.py", line 148, in <module>
    infile = open (infile_name, "r")
IOError: [Errno 2] No such file or directory: 'view_RMTA1a.m8'

Here I attach the command I used: python DIAMOND_specific_organism_retriever.py -I view_RMTA1a.m8 -D nr1_1653.faa -SO 

Could you help me to solve this? any suggestion?

Best,
IO

[Sam Westreich]

Hi Indah,

This looks pretty straightforward; can you confirm that the infile, 'view_RMTA1a.m8', is in the current directory where you're running this command?  If not, you'll need to supply a path to the file with the -I command, instead of just the file name.

Additionally, in your command, you don't have any organism name specified after the -SO flag.  You'll probably want to do so, e.g. 

$ python DIAMOND_specific_organism_retriever.py -I view_RMTA1a.m8 -D nr1_1653.faa -SO Prevotella

Best,

Sam

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Sam Westreich, PMP, PhD

Microbiome Scientist, DNAnexus, 

http://www.mosaicbiome.com