Zhanglab forum

Dear
I encountered a Java exception when trying to run I-TASSER(Previously, I also encountered errors when running wMUSTER and MUSTER, so I removed them from the thread.). Here is my output log.

Your setting for running I-TASSER is:
-pkgdir = /home/dsj/I-TASSER5.1
-libdir = /home/dsj/ITLIB
-java_home = /home/dsj/jre1.7.0_80
-seqname = PatPSK99
-datadir = /home/dsj/Patchouli_gene_family/output/PKSIII/batch_protein/output/PatPSK99/input
-outdir = /home/dsj/Patchouli_gene_family/output/PKSIII/batch_protein/output/PatPSK99
-runstyle = gnuparallel
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = true
-hours = 5
-LBS = false
-EC = false
-GO = false

1. make seq.txt and rmsinp
Your protein contains 486 residues:
> PatPSK99
MPETLPSFSSSVKLKYVKLGYQYLVNHILTFLLIPIIAAVSIETLRLSPDEMLHIWNSLH
LDLLHVLCCSFLIVFIATVYFMSKPRSIYLVDYACYKPPVTCRVPFSTFMEHSRLILKDN
PKSVDFQMRILERSGLGEETCLPPAIHYIPPTPTMEAARGEAEVVIFSCIDSLMQKTGIK
PKDIDILIVNCSLFSPTPSLSAMVVNKYKLRSNIKSYNLSGMGCSAGLISIDLARDLLQV
HPNSHALVISTEIITPNYYQGSERAMLLPNCLFRMGGAAILLSNKRRECSRAKYKLVHVV
RTHKGADDKAYKCVYEQEDPQGKVGINLSKDLMVIAGEALKSNITTIGPLVLPASEQLLF
LFTLIGRKIFNPKWKPYIPDFKQAFEHFCIHAGGRAVIDELQKNLQLSAEHVEASRMTLH
RFGNTSSSSLWYELGYIEAKGRMKKGNRVWQIGFGSGFKCNSAVWKCNRTIKTPTDGPWQ
DCIDRS
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
submit threading jobs first and run pair during threading
3.1 do threading
start gnuparallel threading PPAS
start gnuparallel threading dPPAS
start gnuparallel threading dPPAS2
start gnuparallel threading Env-PPAS
start gnuparallel threading wPPAS
start gnuparallel threading wdPPAS
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 75
at d.a(d.java)
at d.main(d.java)
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 75
at c.b(c.java)
at c.main(c.java)
FORTRAN STOP
3.2 make restraints
without init: /home/dsj/Patchouli_gene_family/output/PKSIII/batch_protein/output/PatPSK99/input/init.MUSTER
without init: /home/dsj/Patchouli_gene_family/output/PKSIII/batch_protein/output/PatPSK99/input/init.wMUSTER
type= easy, n_good=26, M0= 6, M1_for_medm=1.2, n_sg= 6 role=SEQ
1 gap_terminal=N gap_location= 88 by dPPAS
2 gap_terminal=N gap_location= 81 by wdPPAS
3 gap_terminal=N gap_location= 81 by wPPAS
4 gap_terminal=N gap_location= 88 by dPPAS2
5 gap_terminal=N gap_location= 88 by PPAS
6 gap_terminal=N gap_location= 88 by Env-PPAS
7 gap_terminal=N gap_location= 81 by dPPAS
8 gap_terminal=N gap_location= 87 by wdPPAS
9 gap_terminal=N gap_location= 87 by wPPAS
10 gap_terminal=N gap_location= 85 by dPPAS2
11 gap_terminal=N gap_location= 85 by PPAS
12 gap_terminal=N gap_location= 81 by Env-PPAS
domain2=yes
------ n_link_old= 85-------------
------ 2 domain proteins: 85-------------
type=easy----n_temp_use_for_restraints=20
4.1 run simulation
run 15 gnuparallel simulations
run simulation job 1 / 15
run simulation job 2 / 15
run simulation job 3 / 15
run simulation job 4 / 15
run simulation job 5 / 15
run simulation job 6 / 15
run simulation job 7 / 15
run simulation job 8 / 15
run simulation job 9 / 15
run simulation job 10 / 15
run simulation job 11 / 15
run simulation job 12 / 15
run simulation job 13 / 15
run simulation job 14 / 15
run simulation job 15 / 15

I tried both I-TASSER 5.2 and I-TASSER 5.1, but encountered the same issue with both versions.I'm not sure if this will affect my output, but my program ran for five hours and only computed ten simulations.
What can I do to resolve my issue? Thank you for your assistance.

A bioinformatics tool that uses Java for parts of its pipeline (e.g., for threading, structure refinement, or parsing). It often involves multiple scripts and dependencies, which can be executed in parallel to process multiple protein sequences. Crazy Cattle 3D

Would upgrading to a newer version of Java potentially resolve theslope ArrayIndexOutOfBoundsException?

The occurrence of the above-mentioned error should be that when java called the fortran process, the fortran process failed to execute successfully. We need to write time to debug this error. You can use the online version of I-TASSER(https://zhanggroup.org/I-TASSER/) first.

An application used in bioinformatics that makes use of Java in some parts of its process (such as threading, structure refining, or parsing). It often makes use of a large number of scripts and dependencies that can process many protein sequences at once.