itasser suite

[tingting]

Hi,

I have been granted the access to ITASSER suite, and followed the instructions from the link: http://zhanglab.ccmb.med.umich.edu/I-TA ... wnload.php. I am okay with the default nr database, and no need for GO term and PSI-BLAST.

The command line and the output are as follows:

❯ docker run --rm -it \
-v /Users/username/Downloads/I-TASSER5.2/I-TASSERmod:/opt/I-TASSERmod \
-v /Users/username/Downloads/I-TASSER5.2/example:/opt/example \
-v /Users/username/Downloads/I-TASSER5.2/MTX:/root/ITLIB \
itasser:5.2 \
/opt/I-TASSERmod/runI-TASSER.pl \
-pkgdir /opt \
-libdir /root/ITLIB \
-LBS true \
-EC true \
-GO true \
-seqname example \
-datadir /opt/example \
-java_home /usr \
-light true \
-hours 6 \
-outdir /opt/example[/quote]

Your setting for running I-TASSER is:
-pkgdir = /opt
-libdir = /root/ITLIB
-java_home = /usr
-seqname = example
-datadir = /opt/example
-outdir = /opt/example
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = true
-hours = 6
-LBS = true
-EC = true
-GO = true

Your library files are not complete, please download library with the script download_lib.pl

I tried to use the download_lib.pl to download the library, but

--2023-09-07 10:34:14-- ftp://zhanggroup.org/download/nr.tar.gz
=> ‘nr.tar.gz’
Resolving zhanggroup.org (zhanggroup.org)... 141.213.137.249
Connecting to zhanggroup.org (zhanggroup.org)|141.213.137.249|:21... failed: Operation timed out.
Retrying.

I would really appreciate it if someone can help me with this one.

Thanks
tt

[jlspzw]

Dear user,

Please try this link https://zhanggroup.org/ftp/download/nr.tar.gz

Best
IT Team

[tingting]

Hi,

I downloaded the NR dir with the link you sent me before, but I still can not run the script, and the error showed: Your library files are not complete, please download library with the script download_lib.pl.


download process:

> ./download_lib.pl -libdir libdir -P true -B false -N false
> ./download_lib.pl -libdir libdir -P false -B true -N false
and downloaded nr with the link using wget, and uncompressed it with: > tar -zxvf nr.tar.gz

running command:

/lustre1/scratch/351/vsc35107/I-TASSER5.2/I-TASSERmod/runI-TASSER.pl -pkgdir /lustre1/scratch/351/vsc35107/I-TASSER5.2 -libdir /user/leuven/351/vsc35107/ITLIB -LBS true -EC true -GO true -seqname example -datadir /lustre1/scratch/351/vsc35107/I-TASSER5.2/example -java_home /usr -light true -hours 6 -outdir /lustre1/scratch/351/vsc35107/I-TASSER5.2/example

I feel very confused with the error I ran into now, and I would really appreciate it if you can help me with it.

Thanks
tingting

[tingting]

Hi,

You can ignore the last reply. I made minor adjustment, and the output is as follows:

✔ [Sep/18 21:54] vsc35107@tier2-p-login-3 /scratch/leuven/351/vsc35107/I-TASSER5.2/I-TASSERmod $ /lustre1/scratch/351/vsc35107/I-TASSER5.2/I-TASSERmod/runI-TASSER.pl -pkgdir /lustre1/scratch/351/vsc35107/I-TASSER5.2 -libdir /scratch/leuven/351/vsc35107/ITLIB -LBS true -EC true -GO true -seqname seq.fasta -datadir /lustre1/scratch/351/vsc35107/I-TASSER5.2/example -java_home /usr -light true -hours 6 -outdir /lustre1/scratch/351/vsc35107/I-TASSER5.2/example

Your setting for running I-TASSER is:
-pkgdir = /lustre1/scratch/351/vsc35107/I-TASSER5.2
-libdir = /lustre1/scratch/351/vsc35107/ITLIB
-java_home = /usr
-seqname = seq.fasta
-datadir = /lustre1/scratch/351/vsc35107/I-TASSER5.2/example
-outdir = /lustre1/scratch/351/vsc35107/I-TASSER5.2/example
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = true
-hours = 6
-LBS = true
-EC = true
-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 Secondary structure prediction was done before.
2.3 Predict solvent accessibility...
2.4 run pairmod
pair exist
3.1 do threading
start serial threading PPAS
/tmp/vsc35107/ITseq.fasta
/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/PPAS_seq.fasta
Illegal division by zero at /lustre1/scratch/351/vsc35107/I-TASSER5.2/example/PPAS_seq.fasta line 354.
hostname: tier2-p-login-3
starting time: Mon Sep 18 21:55:04 CEST 2023
pwd: /tmp/vsc35107/ITseq.fasta
running zalign .....

start serial threading dPPAS
/tmp/vsc35107/ITseq.fasta
/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/dPPAS_seq.fasta
Illegal division by zero at /lustre1/scratch/351/vsc35107/I-TASSER5.2/example/dPPAS_seq.fasta line 356.
hostname: tier2-p-login-3
starting time: Mon Sep 18 21:55:08 CEST 2023
pwd: /tmp/vsc35107/ITseq.fasta
running zalign .....

start serial threading dPPAS2
/tmp/vsc35107/ITseq.fasta
/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/dPPAS2_seq.fasta
Illegal division by zero at /lustre1/scratch/351/vsc35107/I-TASSER5.2/example/dPPAS2_seq.fasta line 355.
hostname: tier2-p-login-3
starting time: Mon Sep 18 21:55:22 CEST 2023
pwd: /tmp/vsc35107/ITseq.fasta
running zalign .....

start serial threading Env-PPAS
/tmp/vsc35107/ITseq.fasta
/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/Env-PPAS_seq.fasta
Illegal division by zero at /lustre1/scratch/351/vsc35107/I-TASSER5.2/example/Env-PPAS_seq.fasta line 352.
hostname: tier2-p-login-3
starting time: Mon Sep 18 21:55:37 CEST 2023
pwd: /tmp/vsc35107/ITseq.fasta
running zalign .....

start serial threading MUSTER
/tmp/vsc35107/ITseq.fasta
/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/MUSTER_seq.fasta
Illegal division by zero at /lustre1/scratch/351/vsc35107/I-TASSER5.2/example/MUSTER_seq.fasta line 599.
hostname: tier2-p-login-3
starting time: Mon Sep 18 21:55:51 CEST 2023
pwd: /tmp/vsc35107/ITseq.fasta
running Psi-blast .....
running zalign .....
can not handle sec 1 99000


/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/init.wPPAS exists
/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/init.wdPPAS exists
/lustre1/scratch/351/vsc35107/I-TASSER5.2/example/init.wMUSTER exists
only 3 threading programs have output, please check threading programs

The output files are:

✘ [Sep/18 22:07] vsc35107@tier2-p-login-3 /scratch/leuven/351/vsc35107/I-TASSER5.2/example $ ls -l
total 3456
-rw-r----- 1 vsc35107 vsc35107 2338477 Sep 18 21:46 blast.out
-rwxr-x--x 1 vsc35107 vsc35107 11428 Sep 18 21:55 dPPAS2_seq.fasta
-rwxr-x--x 1 vsc35107 vsc35107 11416 Sep 18 21:55 dPPAS_seq.fasta
-rwxr-x--x 1 vsc35107 vsc35107 11324 Sep 18 21:55 Env-PPAS_seq.fasta
-rw-r----- 1 vsc35107 vsc35107 15552 Sep 18 20:19 exp.dat
-rw-r----- 1 vsc35107 vsc35107 168190 Sep 18 21:17 init.wdPPAS
-rw-r----- 1 vsc35107 vsc35107 170174 Sep 18 21:44 init.wMUSTER
-rw-r----- 1 vsc35107 vsc35107 168382 Sep 18 20:52 init.wPPAS
-rw-r----- 1 vsc35107 vsc35107 24666 Sep 18 20:19 mtx
-rwxr-x--x 1 vsc35107 vsc35107 17623 Sep 18 21:55 MUSTER_seq.fasta
-rw-r----- 1 vsc35107 vsc35107 110682 Sep 18 20:31 pair1.dat
-rw-r----- 1 vsc35107 vsc35107 332046 Sep 18 20:31 pair3.dat
-rwxr-x--x 1 vsc35107 vsc35107 11309 Sep 18 21:55 PPAS_seq.fasta
-rw-r----- 1 vsc35107 vsc35107 23027 Sep 18 20:19 psitmp.chk
-rw-r----- 1 vsc35107 vsc35107 23746 Sep 18 20:19 pssm.txt
-rw-r----- 1 vsc35107 vsc35107 19 Sep 18 21:55 rmsinp
-rw-r----- 1 vsc35107 vsc35107 3146 Sep 18 20:19 seq.dat
-rw-r----- 1 vsc35107 vsc35107 155 Jul 28 2014 seq.fasta
-rw-r----- 1 vsc35107 vsc35107 4457 Sep 18 20:19 seq.ss
-rw-r----- 1 vsc35107 vsc35107 158 Sep 18 21:55 seq.txt
-rwxr-x--x 1 vsc35107 vsc35107 11788 Sep 18 20:52 wdPPAS_seq.fasta
-rwxr-x--x 1 vsc35107 vsc35107 17778 Sep 18 21:17 wMUSTER_seq.fasta
-rwxr-x--x 1 vsc35107 vsc35107 11714 Sep 18 20:34 wPPAS_seq.fasta

I suppose this run is unsuccessful and I didn't see any .pdb files with predicted structures listed in the output file.

Could you please tell me how to correct it?

Thanks in advance!
tingting

[jlspzw]

Dear user,

You can test the solution of this ticket.
viewtopic.php?f=3&t=721&sid=8816cacda68 ... 74368469ed

Best
IT Team