Open yusufzaferaydin opened 4 years ago
milot-mirdita
commented
4 years ago The last version I've tried was dssp-2.0.4-linux-amd64 that worked fine.
We can't give support for HHpred currently due to the lack of time and resources, as all grants for the development of the HH-suite were rejected.
yusufzaferaydin
commented
4 years ago It is probably not due to the version of dssp but because of the script in HHblits that prepares the input commandline for dssp. It works for some proteins but not for others. For instance if the fasta filename is 1fdx.fasta that contains
1fdx AYVINDSCIACGACKPECPVNIIQGSIYAIDADSCIDCGSCASVCPVGAPNPED
HHblits produces this error
Error: command '/vol1/apps/dssp/3.1.4/mkdssp -i 1 -o /tmp/XdIE49enjg/rLf13B_wHm.dssp 2> /dev/null' returned error code 1
I think in the above commandline -i should be followed by a pdb filename instead of 1.
However no error is produced if the fasta filename is 1aazb-1-DOMAK.fasta that contains
1aazb-1-DOMAK MFKVYGYDSNIHKCVYCDNAKRLLTVKKQPFEFINIMPEKGVFDDEKIAELLTKLGRDTQIGLTMPQVFAPDGSHIGGFDQLREYFK
Maybe it is related to the length of the protein ID. Thanks.
schdaude
commented
4 years ago Hi, we experienced a similar problem when running the scripts/addss.pl script and narrowed in down to the AppendDsspSequences function in scripts/addss.pl. It checks whether the sequence name matches the pattern for a SCOPe, SCOP, PDB or DALI identifier. If not, the function returns and doesn't add anything. 1aazb-1-DOMAK therefore just returns but 1fdx triggers the regular expression for PDB and proceeds.
Our guess is that when you run the script in a system where the paths specified in HHPaths.pm (pdbdir, dsspdir) are not present, you get the error message you described.
We didn't follow up any further as we only need the PSIPRED prediction and simply supressed the DSSP part by setting dssp in HHPaths.pm to "".
Maybe this helps
:exclamation: Make to check out our User Guide.
Expected Behavior
The -i flag of mkdssp should include a dssp filename
Current Behavior
The following error is produced in which the -i option is set to 1 instead of a pdb filename:
Error: command '/vol1/software/dssp/3.1.4/mkdssp -i 1 -o /tmp/MhEmNhP0FV/F7RKqm9AjW.dssp 2> /dev/null' returned error code 127
Steps to Reproduce (for bugs)
This error is produced by the latest version of HHsuite3 (by HHblits) from github.
HH-suite Output (for bugs)
Please make sure to post the complete output of the tool you called. Please use gist.github.com.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
The latest version of HHblits and HHpred 128 GB RAM Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz Ubuntu 16.04.1 LTS