Hi, thanks for the great software firstly.
Now I want to run COFACTOR in my computer ( Ubuntu 13.10 ) to predict protein functions based on their structures. I downloaded the whole I-TASSER3.0 from http://zhanglab.ccmb.med.umich.edu/I-TASSER/download/download.php, and then run download_lib.pl to download all the databases needed. I randomly downloaded 1cvu.pdb from RCSB, and modified /I-TASSERmod/runCOFACTOR.pl based on my computer (such as $pkgdir, $libdir, $protname, $model, $datadir, $usrname) to see whether my configurations are right or not.
While, the program output the following messages:
Your setting for running COFACTOR is:
-pkgdir = /home/ytan/I-TASSER3.0
-libdir = /home/ytan/I-TASSER3.0/database_download
-protname = 1cvu
-datadir = /home/ytan/I-TASSER3.0/test_one/1cvu
-usrname = ytan
-homoflag = real
-runstyle = serial
-idcut = 1
-LBS =false
-EC = false
-GO = true
run /home/ytan/I-TASSER3.0/test_one/1cvu/1cvu/cofactor/CF_1cvu_1cvu.pl...
Useless use of /d modifier in transliteration operator at /tmp/ytan/profile_1cvu/alignhits.pl line 314.
Use of uninitialized value $AAN in join or string at ./profile_1cvu line 424.
Use of uninitialized value $AAN in join or string at ./profile_1cvu line 425.
Use of uninitialized value $AAN in join or string at ./profile_1cvu line 425.
Use of uninitialized value $AAN in join or string at ./profile_1cvu line 436.
Use of uninitialized value in multiplication (*) at ./profile_1cvu line 289.
Use of uninitialized value in multiplication (*) at ./profile_1cvu line 289.
Use of uninitialized value in multiplication (*) at ./profile_1cvu line 289.
Use of uninitialized value in multiplication (*) at ./profile_1cvu line 289.
I googled the first warning ( Useless use of /d modifier ) and found it was because of a bug of automake1.9. Then I tried automake and automake1.11, but the warning still exists.
As for the second part ( Use of uninitalized value $AAN ) and the third part ( use of uninitalized value in multiplication ), I have no idea how to fix the program.
Despite the above warnings, the program can still give the predicted results. But I am afraid the results would be inaccurate. Could you help me to figure out what the problem is ?
Thanks in advance!