Some files may missing in CR-I-TASSER

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cooper
Posts: 1
Joined: Tue Apr 19, 2022 1:39 am

Some files may missing in CR-I-TASSER

Post by 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.