rajee@ubuntu:~/I-TASSER2.1/I-TASSERmod$ ./runLOMETS.pl -libdir /home/rajee/I-TASSER -seqname seq.fasta -datadir /home/rajee -usrname rajee
Your setting is:
-libdir =/home/rajee/I-TASSER
-seqname =seq.fasta
-datadir =/home/rajee
-usrname =rajee
-tmptop =tmp
-homoflag =benchmark
-idcut =0.3
-ntemp =20
-ntop =10
starting time: Wed Feb 27 09:07:49 PST 2013
pwd: /home/rajee/I-TASSER/I-TASSERmod
1. make seq.txt
2.1 run Psi-blast
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: /home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: @nl�: not found
Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
2.2 run PSSpred
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
cp: cannot stat `psitmp.mtx': No such file or directory
/home/rajee/I-TASSER/PSSpred/PSSpred1: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/PSSpred/PSSpred2: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/PSSpred/PSSpred3: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/PSSpred/PSSpred4: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/PSSpred/PSSpred5: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/PSSpred/PSSpred6: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/PSSpred/PSSpred7: 1: Syntax error: "(" unexpected
cp: cannot stat `mtx': No such file or directory
cp: cannot stat `pssm.txt': No such file or directory
cp: cannot stat `psitmp.chk': No such file or directory
3.1 do threading
/home/rajee/init.PPA
start threading PPA
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
./zalign: 1: ELF: not found
./zalign: 2: @8@@@r: not found
./zalign: 3: r: not found
./zalign: 4: x: not found
./zalign: 5: xjxj��lIN: not found
./zalign: 1: Syntax error: Unterminated quoted string
Illegal division by zero at /home/rajee/PPA_seq.fasta line 353.
hostname: ubuntu
starting time: Wed Feb 27 09:07:50 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
running zalign .....
/home/rajee/init.dPPA
start threading dPPA
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
./zalign: 3: Syntax error: word unexpected (expecting ")")
Illegal division by zero at /home/rajee/dPPA_seq.fasta line 355.
hostname: ubuntu
starting time: Wed Feb 27 09:07:51 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
running zalign .....
/home/rajee/init.dPPA2
start threading dPPA2
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
./zalign: 3: Syntax error: word unexpected (expecting ")")
Illegal division by zero at /home/rajee/dPPA2_seq.fasta line 354.
hostname: ubuntu
starting time: Wed Feb 27 09:07:51 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
running zalign .....
/home/rajee/init.sPPA
start threading sPPA
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
./zalign: 2: Syntax error: word unexpected (expecting ")")
Illegal division by zero at /home/rajee/sPPA_seq.fasta line 351.
hostname: ubuntu
starting time: Wed Feb 27 09:07:51 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
running zalign .....
/home/rajee/init.MUSTER
start threading MUSTER
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
^[[A/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
./svm-predict: 1: Syntax error: "(" unexpected
./svm-predict: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
./zalign: 1: Syntax error: "(" unexpected
Illegal division by zero at /home/rajee/MUSTER_seq.fasta line 585.
hostname: ubuntu
starting time: Wed Feb 27 09:07:52 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
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
/home/rajee/init.wPPA
start threading wPPA
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string/home/rajee/I-TASSER/blast/bin/blastpgp: 2:
@nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
hostname: ubuntu
starting time: Wed Feb 27 09:07:55 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
running Psi-blast .....
JAVA_HOME setting is not correct
/home/rajee/init.wdPPA
start threading wdPPA
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
hostname: ubuntu
starting time: Wed Feb 27 09:07:55 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
running Psi-blast .....
JAVA_HOME setting is not correct
/home/rajee/init.wMUSTER
start threading wMUSTER
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
^[[Acannot open protein
cannot open protein
cannot open protein
cannot open protein
cannot open protein
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
./svm-predict: 1: Syntax error: "(" unexpected
./svm-predict: 1: Syntax error: "(" unexpected
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 1: Syntax error: Unterminated quoted string
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: @nl�: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: �0: not found
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open X��X���� @ @: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ��
X�: not found �
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: cannot open @@: No such file
/home/rajee/I-TASSER/blast/bin/blastpgp: 2: ELF: not found
/home/rajee/I-TASSER/blast/bin/makemat: 2: Syntax error: Unterminated quoted string
mv: cannot stat `psitmp.mtx': No such file or directory
hostname: ubuntu
starting time: Wed Feb 27 09:07:56 PST 2013
pwd: /tmp/rajee/LMseq.fasta
running Psi-blast .....
running Psi-blast .....
running Psi-blast .....
JAVA_HOME setting is not correct
only 0 threading programs have output
Jobs finished!
ending time: Wed Feb 27 09:07:59 PST 2013
cannot remove path when cwd is /tmp/rajee/LMseq.fasta for /tmp/rajee/LMseq.fasta: at ./runLOMETS.pl line 670
how can i rectify it kindly help me