Output

[catastrofia]

Only prophage_tbl.txt as output, no prophage.tbl file on output folder.

[jaumlrc]

I have the same issue as catastrofia. I have run Phispy using the provided phage “160490.1”, using the command line:

../PhiSpy/./PhiSpy.py -i Test_Organism/160490.1/ -o Test-org-OUT -t 25

The following is printed in the screen: Making Test Set... (need couple of minutes) Start Classification Algorithm Using training flag: 25 Done with classification Algorithm Start evaluation... Checking prophages in Test-org-OUT/initial_tbl.txt

Finding repeats in pp 1 from 524682 to 577674 Finding repeats in pp 2 from 769726 to 823679 Finding repeats in pp 3 from 1183686 to 1238452 Finding repeats in pp 4 from 1767552 to 1802690 Threshold for fn is 5 Done!!!

However, in the output dir there are only the files:

prophage_tbl.txt tempRepeatDNA.28913.pp.1.fasta tempRepeatDNA.28913.pp.1.fasta.repeatfinder tempRepeatDNA.28913.pp.2.fasta tempRepeatDNA.28913.pp.2.fasta.repeatfinder tempRepeatDNA.28913.pp.3.fasta tempRepeatDNA.28913.pp.3.fasta.repeatfinder tempRepeatDNA.28913.pp.4.fasta tempRepeatDNA.28913.pp.4.fasta.repeatfinder

There is no prophage.tbl file.

I have cloned the Phispy on 02 May 2018.

Could you provide directions on how to solve this issue?

All the best.

[signetang]

I realize the question was asked a while ago, but a friend recently had the same issue and we found the solution, so I thought I would just share it. Go to the script 'evaluation.py' in the folder 'source'. The very last line of the script has been commented out. Just remove the # and when you run PHISPY again the prophage.tbl should be produced.

[mshakya]

This issue still persists and @signetang recommendation works. I would be curious to know why this was commented out in first place and if its ok to uncomment it. Perhaps, just forgot to uncomment the line?

[linsalrob]

This has now been fixed in the latest code