Solved the problem, will leave thread in case someone else
comes across same thing (put details for resolving it on end of post):
---- problem ----
Hi,
Testing I-Tasser and having problem - run seems to conclude without crashing, but produces no model(s):
-> everything seems fine up to and including trajectory generation,
and I do get zipped trajectory files (... tra.bz2 files), but
closc, combo and other pdb files are not generated and
model files is not generated either
-> I-Tasser was downloaded on 25/11/2013, version 2.1
Full output of run:
CMD: /home/ranko/Development/tools/I-TASSER2.1/I-TASSERmod/runI-TASSER.pl -libdir /home/ranko/Development/tools/I-TASSER2.1 -seqname seq.fasta -datadir /home/ranko/Development/workspace/tests/i-tasser -usrname ranko
Your setting is:
-libdir =/home/ranko/Development/tools/I-TASSER2.1
-seqname =Nrf2_hs_neh1.fa
-datadir =/home/ranko/Development/workspace/tests/i-tasser
-usrname =ranko
-runstyle =serial
-idcut =1
-ntemp =20
-nmodel =5
1. make seq.txt and rmsinp
2.1 run Psi-blast
2.3 run solve
2.3 run solve
2.4 run pairmod
2.4.1 removing homology templates based on and 1
2.4.2 running pair ................
FORTRAN STOP
3.1 do threading
start serial threading PPA
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/PPA_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 13:53:28 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running zalign .....
ending time: Tue Nov 26 14:02:21 GMT 2013
start serial threading dPPA
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/dPPA_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 14:02:23 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running zalign .....
ending time: Tue Nov 26 14:20:58 GMT 2013
start serial threading dPPA2
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/dPPA2_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 14:21:00 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running zalign .....
ending time: Tue Nov 26 14:29:49 GMT 2013
start serial threading sPPA
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/sPPA_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 14:29:51 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running zalign .....
ending time: Tue Nov 26 14:46:24 GMT 2013
start serial threading MUSTER
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/MUSTER_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 14:46:26 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running Psi-blast .....
running zalign .....
./zalign 7.01 0.55 0.66 1.6 -0.99 0.31 0.19 0 1.0 0.39 0.19
==>2lz1A 2lz1A 13.4075253264978 10.9271767776278
2lz1A 2lz1A 63 63
score_flag=1
ending time: Tue Nov 26 15:15:46 GMT 2013
start serial threading wPPA
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/wPPA_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 15:15:48 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running Psi-blast .....
ending time: Tue Nov 26 16:13:59 GMT 2013
start serial threading wdPPA
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/wdPPA_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 16:14:04 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running Psi-blast .....
ending time: Tue Nov 26 17:32:06 GMT 2013
start serial threading wMUSTER
/tmp/ranko/ITNrf2_hs_neh1.fa
/home/ranko/Development/workspace/tests/i-tasser/wMUSTER_Nrf2_hs_neh1.fa
hostname: ranko-ws
starting time: Tue Nov 26 17:32:10 GMT 2013
pwd: /tmp/ranko/ITNrf2_hs_neh1.fa
running Psi-blast .....
running Psi-blast .....
==>2lz1A 2lz1A 16.6000977803961 13.3459721993271
2lz1A 2lz1A 63.78 63.78
score_flag=1
ending time: Tue Nov 26 19:28:25 GMT 2013
3.2 make restraints
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
run simulation job 2 / 14
run simulation job 3 / 14
run simulation job 4 / 14
run simulation job 5 / 14
run simulation job 6 / 14
run simulation job 7 / 14
run simulation job 8 / 14
run simulation job 9 / 14
run simulation job 10 / 14
run simulation job 11 / 14
run simulation job 12 / 14
run simulation job 13 / 14
run simulation job 14 / 14
5.1 do clustering
No. of trajectory files: 62
8.000000 3.500000 12.00000
/bin/cp: cannot stat `./closc*.pdb': No such file or directory
/bin/cp: cannot stat `./combo*.pdb': No such file or directory
5.2 build full-atomic model
Also attached full file list I get after run (I-tasser-run-output.txt)
---- fixing it: -----
-> basically problem was with spicker getting no trajectories as input
(strange enough it doesn't generate any errors if that happens)
because trajectories didn't get unzipped.
-> problem was caused by I-Tasser being unable to access bzip2 (it looks for it
in /usr/bin.
-> apparently I-Tasser does not generate any error messages when it happens
-> once I managed to track problem down, it is easily solved by linking bunzip2 to correct location:
sudo ln -s /bin/bunzip2 . (executed from /usr/bin) resolved it
Note:
-> similar problem can arise with cp command (as I-Tasser looks for it in /usr/bin as well)
Ranko Gacesa,
Institute of Pharmaceutical Sciences,
King's College London