I am receiving index out of bounds errors and a divide by zero error when running runI-TASSER.pl. Here is the command line and console output:
===============================================
time /media/sf_D_DRIVE/home/bill/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -libdir /media/sf_D_DRIVE/home/bill/ITLIB -seqname orf8 -datadir /home/bill/covid-19/orf8 -runstyle gnuparallel -java_home /home/bill/anaconda3
Your setting for running I-TASSER is:
-pkgdir = /media/sf_D_DRIVE/home/bill/I-TASSER5.1
-libdir = /media/sf_D_DRIVE/home/bill/ITLIB
-java_home = /home/bill/anaconda3
-seqname = orf8
-datadir = /home/bill/covid-19/orf8
-outdir = /home/bill/covid-19/orf8
-runstyle = gnuparallel
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false
1. make seq.txt and rmsinp
Your protein contains 121 residues:
> orf8
MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIEL
CVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDF
I
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 MUSTER
start gnuparallel threading wPPAS
start gnuparallel threading wdPPAS
start gnuparallel threading wMUSTER
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 66 out of bounds for length 66
at d.a(d.java)
at d.main(d.java)
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 66 out of bounds for length 66
at c.a(c.java)
at c.main(c.java)
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 101 out of bounds for length 101
at e.main(e.java)
Illegal division by zero at /home/bill/covid-19/orf8/wMUSTER_orf8 line 570.
FORTRAN STOP
3.2 make restraints
without init: /home/bill/covid-19/orf8/init.wMUSTER
type= hard, n_good= 0, M0= 7, M1_for_medm=1.4, n_sg= 0 role=SEQ
domain2=no
type=hard----n_temp_use_for_restraints=50
4.1 run simulation
run 14 gnuparallel 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: 54
8.000000 3.500000 12.00000
5.2 build full-atomic model
6 Estimate local accuracy of models and B-factor
real 275m1.722s
user 1045m52.020s
sys 34m40.134s
==========================================================
The program runs to completion despite the errors. The sequence is identical to QHD43422 from https://zhanglab.ccmb.med.umich.edu/COVID-19/, but the predicted models are not similar.
Linux version:
lsb_release -a ; uname -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 19.10
Release: 19.10
Codename: eoan
Linux bill-VirtualBox 5.3.0-46-generic #38-Ubuntu SMP Fri Mar 27 17:37:05 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Java version:
java -version
openjdk version "11.0.1" 2018-10-16 LTS
OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS)
OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)
Perl version:
perl -v
This is perl 5, version 28, subversion 1 (v5.28.1) built for x86_64-linux-gnu-thread-multi
(with 61 registered patches, see perl -V for more detail)
Thanks
Bill