Hi all,
I'm having what seems to be a unique issue with the first step of I-TASSER 4.0 standalone. Here's what I get after running it through a MATLAB script:
>> itasser;
Your setting for I-TASSER is:
-pkgdir = /media/user/datadrive/itasser/I-TASSERmod
-libdir = /media/user/datadrive/itasser/lib
-java_home = /usr
-seqname = PROTEINX
-datadir = /media/user/datadrive/itasser/data/PROTEINX
-usrname = user
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = true
-EC = true
-GO = true
1. make seq.txt and rmsinp
Your protein contains 409 residues:
cat: /media/user/datadrive/itasser/data/PROTEINX/seq.txt: No such file or directory
2.1 run Psi-blast
cp: cannot stat ‘/media/user/datadrive/itasser/data/PROTEINX/seq.txt’: No such file or directory
sh: 1: /media/user/datadrive/itasser/I-TASSERmod/blast/bin/blastpgp: not found
/media/user/datadrive/itasser/I-TASSERmod/blast/bin/blastpgp is not working properly, please check
So, it looks like the seq.fasta is being read ("Your protein contains 409 residues:"), but then cat isn't working. The only change to the perl script I made is to force LBS, EC, and GO as true by default. Is there something about line 408 to 444 of the runI-TASSER.pl script that could be affecting the fasta to txt conversion, or am I making a stupid mistake somewhere?
EDIT: Eureka! Figure it out and hopefully this will prevent future frustrations. Turns out I had made the seq.fasta file in MATLAB while under root privileges (sudo'd MATLAB startup via terminal in Ubuntu). Changing the permissions back to my standard user allowed for seq.txt to be written to the datadir and everything runs smoothly now.