Closed catastrofia closed 4 years ago
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.
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.
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?
This has now been fixed in the latest code
Only prophage_tbl.txt as output, no prophage.tbl file on output folder.