I-TASSER 5.0: mPSSpred.pl gives error "Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE /" on line 400

Hi everyone,

I've been running I-TASSER on about 250 human protein sequences. All proteins are run in the same way.

It succeeds in 247 cases and fails in 3. The failures all exhibit the same behaviour.

I've run the same 250 proteins 4 times to test the effect of -runstyle and -light, and in all 4 runs, the same 3 proteins fail in the same way. All others succeed.

Incidentally, I-TASSER returns an exit status of 0 in the case when it should probably return a non-zero exit status.

This is the output I see on the stderr in one example (all 3 failed cases are similar):


Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /data/projects/my_project/I-TASSER5.0/PSSpred/mPSSpred.pl line 400.
cp: cannot stat ‘/home/myname/jobs/mytest/results/9b/my_protein/seq.dat’: No such file or directory
FORTRAN STOP
cp: cannot stat ‘/home/myname/jobs/mytest/results/9b/my_protein/seq.dat’: No such file or directory
open: No such file or directory
apparent state: unit 77 named seq.dat
last format: list io
lately reading sequential formatted external IO
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/PPAS_seq.fasta line 354.
cp: cannot stat ‘/home/myname/jobs/mytest/results/9b/my_protein/seq.dat’: No such file or directory
At line 343 of file ppa1.f
Fortran runtime error: No such file or directory
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/dPPAS_seq.fasta line 356.
cp: cannot stat ‘/home/myname/jobs/mytest/results/9b/my_protein/seq.dat’: No such file or directory
At line 343 of file ppa1.f
Fortran runtime error: No such file or directory
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/dPPAS2_seq.fasta line 355.
cp: cannot stat ‘/home/myname/jobs/mytest/results/9b/my_protein/seq.dat’: No such file or directory
At line 354 of file zal3.f
Fortran runtime error: No such file or directory
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/Env-PPAS_seq.fasta line 352.
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /data/projects/my_project/I-TASSER5.0/PSSpred/mPSSpred.pl line 400.
At line 500 of file zal33.f
Fortran runtime error: No such file or directory
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/MUSTER_seq.fasta line 599.
cp: cannot stat ‘/home/myname/jobs/mytest/results/9b/my_protein/seq.dat’: No such file or directory
Exception in thread "main" java.io.FileNotFoundException: seq.dat (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at java.io.FileReader.(FileReader.java:58)
at d.a(d.java)
at d.main(d.java)
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/wPPAS_seq.fasta line 340.
cp: cannot stat ‘/home/myname/jobs/mytest/results/9b/my_protein/seq.dat’: No such file or directory
Exception in thread "main" java.io.FileNotFoundException: seq.dat (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at java.io.FileReader.(FileReader.java:58)
at c.a(c.java)
at c.main(c.java)
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/wdPPAS_seq.fasta line 348.
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /data/projects/my_project/I-TASSER5.0/PSSpred/mPSSpred.pl line 400.
cp: cannot stat ‘seq.dat’: No such file or directory
cp: cannot stat ‘seq.dat’: No such file or directory
Exception in thread "main" java.io.FileNotFoundException: seq.dat (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at java.io.FileReader.(FileReader.java:58)
at e.a(e.java)
at e.main(e.java)
Illegal division by zero at /home/myname/jobs/mytest/results/9b/my_protein/wMUSTER_seq.fasta line 570.

Here is the output on stdout:


Your setting for running I-TASSER is:
-pkgdir = /data/projects/my_project/I-TASSER5.0
-libdir = /data/projects/my_project/ITLIB
-java_home = /usr/local/easybuild/software/Java/1.8.0_71/
-seqname = seq.fasta
-datadir = /home/myname/jobs/mytest/results/9b/my_protein
-outdir = /home/myname/jobs/mytest/results/9b/my_protein
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 1
-light = true
-hours = 5
-LBS = true
-EC = true
-GO = true

1. make seq.txt and rmsinp
Your protein contains 786 residues:
> seq.fasta
SQALRSLYIGTASTSIPLHSHASSHLRTRHFYYHHHHPQPHQYRNPTNDSDHQWDQPI
PKLIHGQNLYIPTFTHFLHTPSSHLNFYHQHHPQPHQYRHQNPCGPHHVGHQQQATHT
LHHTLPTYRDHSHLFHRSCHCNILPDHHYRSNPITPSHHTSHSRSIFLHLLGDSKYSHSH
HPYPRTDGHFCLHPLNANRHYSSTDHDQGHRVHPHSPTNDGNHQWDQPIPKLIHGQNFY
IPTFTHFLNTSSSHPNFYHHHHPQPHQYRHQNPCGPHHLGHQQQATHTLHHTFPTYREQ
SHLFHRSYDCNILSDHHYLSNPITPSDHTSHSHSTFLHLLGDSKYSHSHHHYPHTDGHFC
LHPLNANRHRSSTNNAQGHRVHPHSANNDADHQRDEPSPELIQHSQNLYIPTFTNFLHTP
SSHPNFYRHHPQSHQSRNRHPCGPHHLSHQQQANHTLHHTLLTYREQSLLFHRSYDCNI
LPDHHYLSNPITPSDHTSHSRSTFLHLFGDSKYSHSHHPYPCTDGHFCLHPLNANRHDSS
TDNAQGHRVHPHSANNDADHQRDQPSPELIKHSQNLYIPTFTHFLHTPCSHLNFYHQHH
PQPHQYRNWGACGPHHLSHQQQANPALHHTLPTYRVTTLKATGSIHTAPPMTPTTSGTSQ
SPSSFSMAKTSTSLPYHTSSTHHPEVTPTSTTNITPKHTSTGTRTPVAHTTSATSSKLPT
PFTTHSPPTGSSPISSTGPVTATSFQTTTTYPTPSHSHTTLPTHVPPSSTSLVTPNTHTV
ITHTHA
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 ................
30000 6379375 total lib str & residues
number of observations 14.93992 2.7128680E+07
pair done
3.1 do threading
start serial threading PPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/PPAS_seq.fasta
hostname: myhost
starting time: Thu Oct 20 00:10:16 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....

start serial threading dPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/dPPAS_seq.fasta
hostname: myhost
starting time: Thu Oct 20 00:10:46 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....

start serial threading dPPAS2
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/dPPAS2_seq.fasta
hostname: myhost
starting time: Thu Oct 20 00:11:16 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....

start serial threading Env-PPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/Env-PPAS_seq.fasta
hostname: myhost
starting time: Thu Oct 20 00:11:46 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....

start serial threading MUSTER
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/MUSTER_seq.fasta
hostname: myhost
starting time: Thu Oct 20 00:12:14 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
running zalign .....

start serial threading wPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/wPPAS_seq.fasta
hostname: myhost
starting time: Thu Oct 20 01:12:26 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....

start serial threading wdPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/wdPPAS_seq.fasta
hostname: myhost
starting time: Thu Oct 20 03:27:03 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....

start serial threading wMUSTER
/tmp/myname/ITseq.fasta
/home/myname/jobs/mytest/results/9b/my_protein/wMUSTER_seq.fasta
hostname: myhost
starting time: Thu Oct 20 05:24:26 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
running Psi-blast .....

only 0 threading programs have output, please check threading programs
command: /home/myname/my_project/I-TASSER5.0/I-TASSERmod/runI-TASSER.pl -light true -LBS true -EC true -GO true -nmodel 1 -pkgdir /home/myname/my_project/I-TASSER5.0/ -libdir /home/myname/my_project/ITLIB -seqname seq.fasta -datadir results/9b/my_protein -java_home /usr/local/easybuild/software/Java/1.8.0_71/ -outdir results/9b/my_protein