Missing files in the COFACTOR EC library
Posted: Thu Nov 04, 2021 2:34 pm
Hi,
I was running the standalone COFACTOR and got errors on files missing in the Enzyme library (and additional errors afterward, not sure if they were related to the missing files). The library was downloaded using the "download_lib.pl" script and the "Enzyme" folder has 3,655 pdb files in it. Could anyone help me to figure it out? Thanks in advance! The error messages are as below:
Hostname: localhost
Started : Thu 04 Nov 2021 06:48:27 PM CST
Path : /home/xiaofan/analysis/genome/tools/COFACTOR3
Running pairwise sequence comparisions between templates
Extending TM-align search to complete PDB
Collected: 34
Starting with EC search
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3g61A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1y791.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2z1qB.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2uxwA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1wmwA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3g4dA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3lomA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3npkA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1xg5C.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1jk0A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2rccA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1edoA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2azkA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1ta9B.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2wlaA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3lk5A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2vr2A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1jqnA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1zemA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2bd0A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1rsrB.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2h8oA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1g0oC.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2yyjA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3ffzA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1yfmA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2ftzA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2dh4A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3m9uA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
Starting reverse
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3lomA.pdb': No such file or directory
Cant find /tmp/xiaofan/CF_P69212_523712/JSD_3lomA/3lomA.pdb
/bin/cp: cannot stat '/tmp/xiaofan/CF_P69212_523712/JSD_3lomA/seq.txt': No such file or directory
cat: seq.txt: No such file or directory
[blastpgp] WARNING: SetUpBlastSearch failed.
Segmentation fault (core dumped)
Error in alignhits.pl: blast output file blast.out truncated:
Cant open blast.fasta at ./profile_3lomA line 165.
readline() on closed filehandle PDB at ./bin/COFACTOR.pl line 2090.
Illegal division by zero at ./bin/COFACTOR.pl line 2871.
Best,
Xiaofan
I was running the standalone COFACTOR and got errors on files missing in the Enzyme library (and additional errors afterward, not sure if they were related to the missing files). The library was downloaded using the "download_lib.pl" script and the "Enzyme" folder has 3,655 pdb files in it. Could anyone help me to figure it out? Thanks in advance! The error messages are as below:
Hostname: localhost
Started : Thu 04 Nov 2021 06:48:27 PM CST
Path : /home/xiaofan/analysis/genome/tools/COFACTOR3
Running pairwise sequence comparisions between templates
Extending TM-align search to complete PDB
Collected: 34
Starting with EC search
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3g61A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1y791.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2z1qB.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2uxwA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1wmwA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3g4dA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3lomA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3npkA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1xg5C.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1jk0A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2rccA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1edoA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2azkA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1ta9B.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2wlaA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3lk5A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2vr2A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1jqnA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1zemA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2bd0A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1rsrB.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2h8oA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1g0oC.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2yyjA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3ffzA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/1yfmA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2ftzA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/2dh4A.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3m9uA.pdb': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
Starting reverse
/bin/cp: cannot stat '/home/xiaofan/analysis/genome/tools/COFACTOR3/ITLIB/Enzyme/3lomA.pdb': No such file or directory
Cant find /tmp/xiaofan/CF_P69212_523712/JSD_3lomA/3lomA.pdb
/bin/cp: cannot stat '/tmp/xiaofan/CF_P69212_523712/JSD_3lomA/seq.txt': No such file or directory
cat: seq.txt: No such file or directory
[blastpgp] WARNING: SetUpBlastSearch failed.
Segmentation fault (core dumped)
Error in alignhits.pl: blast output file blast.out truncated:
Cant open blast.fasta at ./profile_3lomA line 165.
readline() on closed filehandle PDB at ./bin/COFACTOR.pl line 2090.
Illegal division by zero at ./bin/COFACTOR.pl line 2871.
Best,
Xiaofan