Missing files in the COFACTOR EC library

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mito1983
Posts: 3
Joined: Thu Nov 04, 2021 2:23 pm

Missing files in the COFACTOR EC library

Post by mito1983 »

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
xiaogenz
Posts: 157
Joined: Sun Apr 25, 2021 12:02 am

Re: Missing files in the COFACTOR EC library

Post by xiaogenz »

This is because some proteins are removed from the library as they have no function annotations (or they had function annotations before but were removed later). You can ignore the "error" since it will not affect the final result. However, you can download the completed Enzyme library to replace the old one if you want to remove this error.
The Enzyme library can be downloaded at:
https://zhanggroup.org/BioLiP/download/ ... e2.tar.bz2
Please let me know if you have any questions.
mito1983
Posts: 3
Joined: Thu Nov 04, 2021 2:23 pm

Re: Missing files in the COFACTOR EC library

Post by mito1983 »

Thanks for your reply! I still have two questions:

1. the link you provided points to the same library file I have, which does not contain these missing proteins.

2. besides the missing files, I also have the following errors, could you take a look?

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.

Thanks!
Xiaofan
xiaogenz
Posts: 157
Joined: Sun Apr 25, 2021 12:02 am

Re: Missing files in the COFACTOR EC library

Post by xiaogenz »

Sorry! The link should be https://zhanggroup.org/BioLiP/download/ ... e2.tar.bz2
Please try it again. I think the error will be removed after updating the library.
mito1983
Posts: 3
Joined: Thu Nov 04, 2021 2:23 pm

Re: Missing files in the COFACTOR EC library

Post by mito1983 »

This new library file works perfectly. Thanks very much!

I also ran the standalone version of MetaGO, and got the following error message:

run GOfreq and PPI2GO
/home/xiaofan/analysis/genome/tools/MetaGO/bin/GOfreq/run_GOfreq.py /home/xiaofan/analysis/genome/tools/MetaGO/P69212/config.py
/home/xiaofan/analysis/genome/tools/MetaGO/bin/GOfreq/run_PPI2GO.py /home/xiaofan/analysis/genome/tools/MetaGO/P69212/config.py
cp: cannot stat '/home/xiaofan/analysis/genome/tools/MetaGO/bin/GOfreq/dat/protein.links.shelve*': No such file or directory
mapped to string ID: 316385.ECDH10B_1733,316407.1742634,198214.SF1621,469008.ECD_01569,155864.Z2594,511145.b1600,469008.B21_01559,481805.EcolC_2030,362663.ECP_
1544
mapped to 738 partners
Error: [blastdbcmd] 469008.B21_01558: OID not found
Error: [blastdbcmd] 469008.B21_01774: OID not found
Error: [blastdbcmd] 469008.ECD_01786: OID not found
Error: [blastdbcmd] 469008.ECD_01568: OID not found
155864.Z4599
511145.b1642
316385.ECDH10B_2689
316407.85676937
316385.ECDH10B_2686
......
updating parent level 3 for C
updating parent level 4 for C
updating parent level 0 for F
updating parent level 1 for F
updating parent level 2 for F
updating parent level 3 for F
updating parent level 4 for F
updating parent level 5 for F
combining GO prediction for .
Can't "last" outside a loop block at ./bin/runMetaGO.pl line 101.

It seems that the analysis finished OK, and I got the result files ("lr_GOfreqPPICofactor_BP/MF/CC"). Are these error messages harmless?

Best,
Xiaofan
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