I-TASSER: bzip2: Can't open input file rep*.tra: No such file or directory.

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Moderator: robpearc

vitamin
Posts: 4
Joined: Fri Apr 30, 2021 3:00 pm

I-TASSER: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by vitamin »

Dear developers and community!

A) Preliminary note:
- Thank you so much for this great tool!
- The answer to my question likely had been answered in the previous forum. But the answers (comments) to these posts are not available any more.

B) Problem description:
- I-TASSER calculation fails
- key Error message:
"bzip2: Can't open input file rep*.tra: No such file or directory."

C) System:
I-TASSER 5.1
Debian 10, up to date
installed RAM: 16 GB

D) Shell log: see [1]

E) already checked:
- no lack of disk space
- no lack of RAM
- no simultaneously instances of I-TASSER running parallel

F) reproducibility: yes


Thank you!



Attachment
[1]
./runI-TASSER.pl -libdir /itasserlib -seqname prot -datadir /debug

Your setting for running I-TASSER is:
-pkgdir = /itasser/I-TASSER5.1
-libdir = /itasserlib
-java_home = /usr
-seqname = prot
-datadir = /debug
-outdir = /debug
-runstyle = serial
-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 183 residues:
> prot
MRKIVVAAIAVSLTTVSITASASADPSKDSKAQVSAAEAGITGTWYNQLGSTFIVTAGAD
GALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQY
VGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDA
VQQ
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 ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 26.62686 2675120.
pair done
3.1 do threading
start serial threading PPAS
/tmp/root/ITprot
/debug/PPAS_prot
hostname: localhost
starting time: Fri 30 Apr 2021 04:05:05 PM UTC
pwd: /tmp/root/ITprot
running zalign .....
ending time: Fri 30 Apr 2021 04:11:09 PM UTC

start serial threading dPPAS
/tmp/root/ITprot
/debug/dPPAS_prot
hostname: localhost
starting time: Fri 30 Apr 2021 04:11:10 PM UTC
pwd: /tmp/root/ITprot
running zalign .....
ending time: Fri 30 Apr 2021 04:22:20 PM UTC

start serial threading dPPAS2
/tmp/root/ITprot
/debug/dPPAS2_prot
hostname: localhost
starting time: Fri 30 Apr 2021 04:22:21 PM UTC
pwd: /tmp/root/ITprot
running zalign .....
ending time: Fri 30 Apr 2021 04:31:56 PM UTC

start serial threading Env-PPAS
/tmp/root/ITprot
/debug/Env-PPAS_prot
hostname: localhost
starting time: Fri 30 Apr 2021 04:31:57 PM UTC
pwd: /tmp/root/ITprot
running zalign .....
ending time: Fri 30 Apr 2021 04:46:26 PM UTC

start serial threading MUSTER
/tmp/root/ITprot
/debug/MUSTER_prot
hostname: localhost
starting time: Fri 30 Apr 2021 04:46:28 PM UTC
pwd: /tmp/root/ITprot
running Psi-blast .....
running zalign .....
#2 residue inconsistent ! /itasserlib/DEP/6lnwA.dep 129 495

==>1n9mC 1n9mC 12.8559475624466 9.47940515858143
1n9mC 1n9mC 68 68
score_flag=1
ending time: Fri 30 Apr 2021 05:02:22 PM UTC

start serial threading wPPAS
/tmp/root/ITprot
/debug/wPPAS_prot
hostname: localhost
starting time: Fri 30 Apr 2021 05:02:23 PM UTC
pwd: /tmp/root/ITprot
running Psi-blast .....
ending time: Fri 30 Apr 2021 05:22:14 PM UTC

start serial threading wdPPAS
/tmp/root/ITprot
/debug/wdPPAS_prot
hostname: localhost
starting time: Fri 30 Apr 2021 05:22:15 PM UTC
pwd: /tmp/root/ITprot
running Psi-blast .....
ending time: Fri 30 Apr 2021 05:56:56 PM UTC

start serial threading wMUSTER
/tmp/root/ITprot
/debug/wMUSTER_prot
hostname: localhost
starting time: Fri 30 Apr 2021 05:56:57 PM UTC
pwd: /tmp/root/ITprot
running Psi-blast .....
running Psi-blast .....
==>1n9mC 1n9mC 15.6887499543776 11.9358070121161
1n9mC 1n9mC 68.31 68.31
score_flag=1
ending time: Fri 30 Apr 2021 06:38:29 PM UTC

3.2 make restraints
type= easy, n_good=40, M0= 8, M1_for_medm=1.6, n_sg= 8 role=SEQ
domain2=no
type=easy----n_temp_use_for_restraints=20
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 2 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 3 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 4 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 5 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 6 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 7 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 8 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 9 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 10 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 11 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 12 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 13 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 14 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files: 0
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: I-TASSER: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by robpearc »

The error appears to be due to the I-TASSER folding simulations failing to generate the structure decoy files (rep*.tra), although the exact error for this isn't apparent from the output. If you zip your data directory and send it to robpearc@umich.edu, I will look at the issue further.
vitamin
Posts: 4
Joined: Fri Apr 30, 2021 3:00 pm

Re: I-TASSER: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by vitamin »

Thanks!
Pedro Queiroz
Posts: 1
Joined: Sat Jun 05, 2021 1:26 pm

Re: I-TASSER: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Pedro Queiroz »

Dear community and developers,

Hope you are all doing well.

I got the same error message while trying to run the I-TASSER suite, except my system settings were as follows:

I-TASSER 5.0
Ubuntu 20.04 LTS
Installed RAM: 16 Gb

Error message:
3.2 make restraints
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 2 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 3 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 4 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 5 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 6 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 7 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 8 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 9 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 10 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 11 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 12 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 13 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 14 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files: 0
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