Some files may missing in CR-I-TASSER

[cooper]

I crashed it when learning CR-I-TASSER. the error show "Exception in thread "main" java.io.FileNotFoundException: /data03/lipan/Protein_Structure/CR-I-TASSER/DEP/7a4aA.dep (No such file or directory)"


Step 1.
I have downloaded CR-I-TASSER-1.0.tar.bz2 and CR-I-TASSER library. My OS is CentOS Linux release 7.6.1810 (Core).

Step 2.
I extract them and install accord to https://zhanggroup.org//CR-I-TASSER/sta ... MANUAL.txt

Step 3.
I mkdir path: /data2/home/liubinghua/cr_i_tasser_T0886_dom1

Step 4.
copy file CR-I-TASSER-1.0/example/T0886_dom1/inputmap.map and CR-I-TASSER-1.0/example/T0886_dom1/seq.fasta to /data2/home/liubinghua/cr_i_tasser_T0886_dom1

Step 5.
run command like this:

cd /data2/home/liubinghua/cr_i_tasser_T0886_dom1

/data2/home/liubinghua/cr_i_tasser/CR-I-TASSER-1.0/I-TASSERmod/runI-TASSER.pl \
-runstyle gnuparallel \
-libdir /data03/lipan/Protein_Structure/CR-I-TASSER \
-seqname seq.fasta \
-mapname inputmap.map \
-datadir $(pwd) \
-outdir ./ \
-python2 ~/mambaforge/envs/py27_37/bin/python2 \
-python3 ~/mambaforge/envs/py37/bin/python3


Step 6.
About one hour later, errors show that 7a4aA.dep not find, the details below:
sh: line 1: 155421 Segmentation fault /data2/home/liubinghua/mambaforge/envs/py37/bin/python3 /data2/home/liubinghua/cr_i_tasser/CR-I-TASSER-1.0/contact/ResTriplet/deeppre.py /tmp/liubinghua/CITeCEthreader_seq.fasta//deepmsa_protein.aln /tmp/liubinghua/CITeCEthreader_seq.fasta//deepmsa.contact
At line 697 of file zal3.f
Fortran runtime error: No such file or directory
Illegal division by zero at /data2/home/liubinghua/cr_i_tasser_T0886_dom1/CITMUSTER_seq.fasta line 599.
Exception in thread "main" java.io.FileNotFoundException: /data03/lipan/Protein_Structure/CR-I-TASSER/DEP/7a4aA.dep (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.<init>(FileInputStream.java:138)
at java.io.FileInputStream.<init>(FileInputStream.java:93)
at java.io.FileReader.<init>(FileReader.java:58)
at c.a(c.java)
at c.main(c.java)
Exception in thread "main" java.io.FileNotFoundException: /data03/lipan/Protein_Structure/CR-I-TASSER/DEP/7a4aA.dep (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.<init>(FileInputStream.java:138)
at java.io.FileInputStream.<init>(FileInputStream.java:93)
at java.io.FileReader.<init>(FileReader.java:58)
at e.a(e.java)
at e.main(e.java)
FORTRAN STOP

I crash in the issue, any help would be deeply appreciated.

Thank yo for your time.

[carolinamay]

If available, try running CR-I-TASSER in a debug mode or with verbose logging to get more detailed error messages. This may provide additional insights into where the process is failing. Check out geometry dash lite to know more information.

[responsivecats]

Using several threading alignment techniques, I-TASSER first recognizes structural templates from the PDB. Simulations of iterative fragment assembly are then used to build full-length structural retro bowl models. Finally, the projected structural models are compared with known proteins in the function databases to get the functional insights.