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I am trying to use Porter5 to run protein secondary structure prediction on a FASTA file containing a bunch of protein sequences. I am using a Linux machine.

For starters, I decided to try using the example file that gets downloaded along with Porter5, called 2FLGA.fasta. The command I used was the one I found on the GitHub page for Porter5 (https://github.com/mircare/Porter5/)

$ python3 Porter5.py -i example/2FLGA.fasta --cpu 4

I got the following error message:

sh: 1: /home/user/ncbi-blast-2.8.1+/bin/psiblast: not found
PSI-BLAST executed in 0.01s
wc: example/2FLGA.fasta.psi: No such file or directory
awk: cannot open example/2FLGA.fasta.psi (No such file or directory)
HHblits executed in 0.01s
Traceback (most recent call last):
  File "/home/user/Porter5/scripts/process-alignment.py", line 37, in <module>
    sequences = lines[0] = len(lines) - 1
IndexError: list assignment index out of range
Traceback (most recent call last):
  File "Porter5.py", line 80, in <module>
    flatpsi_ann = open(filename+".flatpsi.ann", "r").readlines()
FileNotFoundError: [Errno 2] No such file or directory: 'example/2FLGA.fasta.flatpsi.ann'

After PSI-BLAST, the Porter5 script is expecting an output file called 2FLGA.fasta.psi. I checked the example directory and it contains an output file called 2FLGA.fasta.flatpsi.

I'm not sure what to do here. I don't want to try modifying any of the Porter5 scripts to look for .flatpsi files instead of .psi files because I am a beginner at programming, and I don't want all hell to break loose by tampering with the code.

Could someone please help me with this? Any help is appreciated.

(There are a bunch of errors to negotiate with later but I'll see about those after dealing with the first one.)

David Jacquel
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Bertram Wooster
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1 Answers1

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I am the author of Porter5 and I generally recommend to open an issue straight on GitHub since I don't get any notification otherwise.

It looks like the path of psiblast is wrong (first line of your error message). You can check that with the following command:

$ ls /home/user/ncbi-blast-2.8.1+/bin/psiblast

Also, the path for the executable or the database of HHblits is wrong, or maybe both. You can check that as follow (within Porter5/):

$ cat scripts/config.ini

You can either edit scripts/config.ini or run the following command until Porter5 runs succesfully:

$ python3 Porter5.py -i example/2FLGA.fasta --cpu 4 --setup

(The .flatpsi is an intermediate file, it doesn't contain a valid representation if HHblits doesn't run succesfully)

Mirko Torrisi
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