Hi everyone,
I'm testing I-TASSER 5.0 on our local HPC cluster. I've submitted a single job on the cluster, which runs the following command:
runI-TASSER.pl -light true -LBS true -GO true -nmodel 1 -pkgdir /home/myname/myproject/I-TASSER5.0/ -libdir /home/myname/myproject/ITLIB -seqname seq.fasta -datadir example -java_home /usr/local/easybuild/software/Java/1.8.0_71/ -outdir results
I installed I-TASSER following the instructions here:
http://zhanglab.ccmb.med.umich.edu/I-TASSER/download/README5.0.txt
Including running the download_lib.pl script.
It runs for quite a while and then ends with an error.
It seems to go wrong after the step "7 run COACH to predict function: Ligand-binding site,GO terms..."
I search for some of the error messages, and found a previous post on the Zhang Lab forums, but I don't understand how the issue was resolved:
http://zhanglab.ccmb.med.umich.edu/bbs/?q=node/3798
(see particularly the part in that previous thread about "At line 210 of file EClocal.f (unit = 40, file = '')")
Below is the full output stream from my I-TASSER job. Apologies for the long post, but I assume it would be best if you saw all the output.
Something strange happens at the end, where the job scheduler (SLURM) kills the job because it uses too much memory (even though I have the job 8GB of RAM, which I presume should be enough for this test case).
Note that I did not set the command line flag "-EC true", and I wonder whether I should have done that?
I appreciate any help you can provide.
Regards,
Bernie Pope
---- start of I-TASSER output ----
Your setting for running I-TASSER is:
-pkgdir = /data/projects/myproject/I-TASSER5.0
-libdir = /data/projects/myproject/ITLIB
-java_home = /usr/local/easybuild/software/Java/1.8.0_71/
-seqname = seq.fasta
-datadir = /home/myname/jobs/test_i-tasser/example
-outdir = /home/myname/jobs/test_i-tasser/results
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 1
-light = true
-hours = 5
-LBS = true
-EC = false
-GO = true
1. make seq.txt and rmsinp
Your protein contains 143 residues:
> seq.fasta
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
2.1 run Psi-blast
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
2.4.2 running pair ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 27.03459 1658491.
pair done
3.1 do threading
start serial threading PPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/PPAS_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Sun Sep 25 22:49:21 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Sun Sep 25 23:08:05 AEST 2016
start serial threading dPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/dPPAS_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Sun Sep 25 23:08:06 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Sun Sep 25 23:47:05 AEST 2016
start serial threading dPPAS2
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/dPPAS2_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Sun Sep 25 23:47:07 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Mon Sep 26 00:03:33 AEST 2016
start serial threading Env-PPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/Env-PPAS_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Mon Sep 26 00:03:35 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Mon Sep 26 00:43:24 AEST 2016
start serial threading MUSTER
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/MUSTER_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Mon Sep 26 00:43:26 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
running zalign .....
==>1rilA 1goaA 20.263281434272 15.7768355649279
1rilA 1goaA 26 34
score_flag=2
ending time: Mon Sep 26 01:08:45 AEST 2016
start serial threading wPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/wPPAS_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Mon Sep 26 01:08:46 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
ending time: Mon Sep 26 01:49:41 AEST 2016
start serial threading wdPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/wdPPAS_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Mon Sep 26 01:49:42 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
ending time: Mon Sep 26 02:24:22 AEST 2016
start serial threading wMUSTER
/tmp/myname/ITseq.fasta
/home/myname/jobs/test_i-tasser/example/wMUSTER_seq.fasta
hostname: myhost005.mydomain.edu
starting time: Mon Sep 26 02:24:23 AEST 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
running Psi-blast .....
==>1rilA 1goaA 26.4437633700093 20.5973049606454
1rilA 1goaA 26.57 34.97
score_flag=2
ending time: Mon Sep 26 03:17:46 AEST 2016
3.2 make restraints
type= easy, n_good=40, M0= 8, M1_for_medm=1.6, n_sg= 8 role=SEQ
domain2=no
type=easy----n_temp_use_for_restraints=20
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
5.2 build full-atomic model
6 Estimate local accuracy of models and B-factor
7 run COACH to predict function: Ligand-binding site,GO terms...
/data/projects/myproject/I-TASSER5.0/I-TASSERmod/runCOACH.pl -pkgdir /data/projects/myproject/I-TASSER5.0 -libdir /data/projects/myproject/ITLIB -runstyle serial -protname seq.fasta -model model1.pdb -datadir /home/myname/jobs/test_i-tasser/example -homoflag real -idcut 1 -LBS true -EC false -GO true
Useless use of /d modifier in transliteration operator at /tmp/myname/JSD_qury/parse_blast.pl line 315.
At line 210 of file COACH/COFACTOR/EClocal.f (unit = 40, file = '')
Fortran runtime error: File 'list' does not exist
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
Use of uninitialized value in multiplication (*) at /home/myname/jobs/test_i-tasser/example/model1/cofactor/CF_seq.fasta_model1.pl line 1291.
cp: cannot stat ‘ECsearchresult_*’: No such file or directory
rm: cannot remove ‘/tmp/myname/CF_seq.fasta_model1’: Directory not empty
Useless use of /d modifier in transliteration operator at ./parse_blast.pl line 315.
slurmstepd: error: Exceeded step memory limit at some point.