SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
issues on running ExomeCNV emilyjia2000 Bioinformatics 11 01-27-2015 05:16 AM
Any tool for SNP functionality prediction? Jluis Bioinformatics 2 04-09-2013 11:11 PM
Suggest a dbSNP annotation and cSNP prediction tool vishakha.more17 Bioinformatics 1 03-14-2011 09:42 AM
Issues in running sff_extract yy01 Bioinformatics 3 09-23-2010 07:58 AM

Reply
 
Thread Tools
Old 01-08-2014, 09:07 PM   #1
bio_informatics
Senior Member
 
Location: USA

Join Date: Nov 2013
Posts: 182
Default issues in running prof protein prediction tool

I have profphd installed successfully in usr/path.

When I run
Quote:
prof /usr/share/profphd/prof/exa/1ppt.f
I get correct file.
But when I try to run,

Quote:
prof sra.fas 3 doHtmtop
where sra.fas is the input fasta file, I get the below error.
Quote:
substr outside of string at /usr/share/perl5/RG/Utils/Copf.pm line 2401, <FHIN_convFastamul2msf> line 70.
Use of uninitialized value in concatenation (.) or string at /usr/share/perl5/RG/Utils/Copf.pm line 2401, <FHIN_convFastamul2msf> line 70.
substr outside of string at /usr/share/perl5/RG/Utils/Copf.pm line 2401, <FHIN_convFastamul2msf> line 70.
Use of uninitialized value in concatenation (.) or string at /usr/share/perl5/RG/Utils/Copf.pm line 2401, <FHIN_convFastamul2msf> line 70.
*** ERROR profrotRd: after protRdAli, fileIn=sra.fas,
*** message from sbr:
*** ERROR protRdAli: failed conversion to HSSP
ok lib-col:sysRunProg

*** ERROR prof: line number of error=113
*** ERROR failed prof:full:doOne dbfile=sra.fas, chain=*!
*** ERROR msg from where it failed:
*** ERROR doOne: reading db=sra.fas, chain=*! (&protRd)
line=1436
*** ERROR protRd: *** ERROR profrotRd: after protRdAli, fileIn=sra.fas,
*** message from sbr:
*** ERROR protRdAli: failed conversion to HSSP
ok lib-col:sysRunProg

*** ERROR doOne: reading db=sra.fas, chain=*! (&protRd)
line=1436
*** ERROR protRd: *** ERROR profrotRd: after protRdAli, fileIn=sra.fas,
*** message from sbr:
*** ERROR protRdAli: failed conversion to HSSP
ok lib-col:sysRunProg
at /usr/share/profphd/prof/scr/lib/lib-prof.pl line 107.
prof::assAbort("failed prof:full:doOne dbfile=sra.fas, chain=*!", 113, "*** ERROR doOne: reading db=sra.fas, chain=*! (&protRd)\x{a}line="...) called at /usr/share/profphd/prof/scr/lib/prof.pm line 112
prof::full("/usr/share/profphd/", "/usr/share/profphd/prof/", "/usr/share/profphd/prof/scr/CONFprof.pl", "LINUX", "prof", "neural network switching", "list_of_files (or single file) parameter_file", 2, "hssp,dssp,msf,saf,fastamul,pirmul,fasta,pir,gcg,swiss", ...) called at /usr/bin/prof line 170
I cannot understand how I to give an input file which is not present in
Quote:
/usr/share/profphd/prof
and get an output.

Please help me.
bio_informatics is offline   Reply With Quote
Reply

Tags
profphd, transmembrane domain

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO