Error: Inconsistent alignment found

[mtnouchi]

Hello,

I used ps_scan.pl to search for motifs in a protein against PROSITE release 2021_03, but the program crashed with the following error:

Error: Inconsistent alignment found in alignment 2 - no list produced.
       Alignement should be from 247 to 170!
Thread 107 : Internal error xalip reported no possible alignment for sequence 3(0) (nali=-1)!
>seq for pfscan
Segmentation fault (core dumped)
Could not execute /usr/local/bin/pfscanV3 --matrix-only -o4 -L-1 prosite.dat /tmp/ps569600-2.tmp  > /tmp/ps569600-1.tmp: Inappropriate ioctl for device at ps_scan.pl line 1751.

Here are the details of the run:

• ps_scan.pl: Revision 1.90

• pfscanV3: I downloaded pftools3-3.2.6 and built it following the instructions in INSTALL. According to make test, the installation was done properly. A series of commands were installed in /usr/local/bin/

• ps_scan.pl & pfscanV3: This error was reproduced with the docker image sibswiss/pftools:3.2.6.

• execution command:

  perl ps_scan.pl -o epff -s --pfscan /usr/local/bin/pfscanV3 test.faa > test.epff
  

  With the older version, there was no error (no hit found, either).

  perl ps_scan.pl -o epff -s --pfscan /usr/local/bin/pfscan test.faa > test.epff
  

• The input sequence: It seems that the problem occurs when test.faa contains the following.

  >YAL049C
  MASNQPGKCCFEGVCHDGTPKGRREEIFGLDTYAAGSTSPKEKVIVILTDVYGNKFNNVL
  LTADKFASAGYMVFVPDILFGDAISSDKPIDRDAWFQRHSPEVTKKIVDGFMKLLKLEYD
  PKFIGVVGYCFGAKFAVQHISGDGGLANAAAIAHPSFVSIEEIEAIDSKKPILISAAEED
  HIFPANLRHLTEEKLKDNHATYQLDLFSGVAHGFAARGDISIPAVKYAKEKVLLDQIYWF
  NHFSNV
  

Here I have shown a minimal input that reproduces the error. In practice, however, I am scanning so many sequences that it is impractical to exclude error-causing inputs. Any suggestions on how to handle this?

Thank you.

[smoretti]

Hi
we would try to find what happens.
@euphemizm an idea?

[smoretti]

@beatrice79 ?

[smoretti]

Hi
could you retry your input on pftools version 3.2.12?

A number of processor affinity issues have been fixed in the meantime.

[mtnouchi]

Hello,

Thanks for taking the trouble to address such very tricky issues.
But, unfortunately, the same error appeared again in version 3.2.12... :(