Error when running PhiSpy

Question

[bioinfoSeeker]

I am running the tutorial from https://github.com/linsalrob/PhiSpy After following the instructions, I ran the command

./PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25

I get the following error message

Making Test Set... (need couple of minutes)
   cant open file 1
   error: Shannon does not work
   The input organism is too small to predict prophages. Please consider large contig (having at least 40 genes) to use PhiSpy.

I then ran PhiSpy on another RAST annotated genbank directory of another WGS assembly, and I still get the same error message. I have the versions of Python, biopython, gcc and randomForest as per spec.

Any suggestions?

[Tonor]

It seems to complain that it can't open a file first, so the first thing to check is that the files exist - does the folder Test_Organism/160490.1/ exist and located in the directory you are running PhiSpy from? Are there files in there? Does output_directory need to be created before running? If so is it there?

[WouterDeCoster]

I started reading the code and didn't get very happy by that...

[Tonor]

The Shanon does not work error, looks like its triggered just after here:

a = input_shannon_mer(INSTALLATION_DIR+'data/mer_ORF_list.txt')

So would guess it can't find data/mer_ORF_list.txt - does that file/folder exist?

The INSTALLATION_DIR is defined here:

INSTALLATION_DIR = argv[0]
    if '/' in argv[0]:
        INSTALLATION_DIR = INSTALLATION_DIR[0:len(INSTALLATION_DIR)-INSTALLATION_DIR[::-1].find('/')]
    else:
        INSTALLATION_DIR = ''

Instructions to run are:

1. Download the example Organism directory (Test_Organism.zip) from http://sourceforge.net/projects/phispy/files/
2. Uncompress Test_Organism.zip
3. Move 'Test_Organism' to PhiSpy-X.X directory
4. % cd PhiSpy-X.X
5. % ./PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25

Only thing I can think off is either Test_Organism doesn't exist or its not picking up the installation dir properly

[WouterDeCoster]

My guess was the second option but didn't look too long at it.

[Tonor]

@brindha, you could maybe try:

PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25

Or

/Full/Path/To/Folder/PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25

[bioinfoSeeker]

Thanks for your reply. The Test_Organism.zip was obtained from https://github.com/linsalrob/EdwardsLab/blob/master/PhiSpy/Test_Organism.zip It does not contain the Test_Organism/160490.1/data/mer_ORF_list.txt or even the Test_Organism/160490.1/data directory or the Test_Organism/160490.1/data/trainingSet directory. Therefore, I downloaded this separately from https://github.com/linsalrob/EdwardsLab/tree/master/PhiSpy/data into a new subdirectories /data and /data/trainingSet within Test_Organism/160490.1/

I get the following error when I run it.

     ./PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25 
Making Test Set... (need couple of minutes) 
Start Classification Algorithm 
Using training flag:  25 Traceback (most recent call last):  
File "./PhiSpy.py", line 157, in <module>
        start_propgram(sys.argv)   File "./PhiSpy.py", line 155, in start_propgram
        call_phiSpy(organismPath,output_dir,trainingFlag,INSTALLATION_DIR,args_parser.evaluate, args_parser.number, args_parser.window_size,args_parser.quiet,args_parser.keep)   File "./PhiSpy.py", line 31, in call_phiSpy
        classification.call_classificaton(organismPath,output_dir,trainingFlag,INSTALLATION_DIR) File "./source/classification.py", line 249, in call_classificaton
        call_randomForest_generic(output_dir+'testSet.txt',trainingFlag,output_dir+'classify.txt',INSTALLATION_DIR) File "./source/classification.py", line 22, in call_randomForest_generic
        x = find_training_genome(trainingFlag,INSTALLATION_DIR)   File "./source/classification.py", line 15, in find_training_genome
        if int(temp[0]) == trainingFlag: ValueError: invalid literal for int() with base 10: ''

[WouterDeCoster]

And what about /Full/Path/To/Folder/PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25 ?

[bioinfoSeeker]

Tried that command as suggested with the full path. It still gives the same error that I have captured in my earlier comment.

I then tried running PhiSpy with another genome directory (10479.4 ) downloaded from the database linked in ReadMe.md. I continue to get the same errors. Moreover any genome directory does not seem have the /data and /data/trainingSet folders that the python script refers to.

Do you run PhiSpy yourself of late? Have you encountered these errors I seem to get? Any help would be appreciated.

[WouterDeCoster]

I never used it, just making guesses :)

[bioinfoSeeker]

Bumping this post up, if it is okay.

Pls see the thread above on my reply/query on this error.