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rlabduke / MolProbity

Protein and nucleic acid validation service
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Command line options not working - offline #20

Open jthornton-0 opened 2 years ago

jthornton-0 commented 2 years ago

Hello, the IT department at my University have been trying to install MolProbity onto our closed-system supercomputer. The Reduce and Probe executables work as expected with no errors (thank you, they're really useful for my research!!), but all of the executables within molprobity/2019/molprobity/cmdline/ do not work as expected.

For example, after loading MolProbity as a module (PATH is the redacted path to the MolProbity folder):

$ clashscore PHP Warning: include_once(/PATH/molprobity/2019/molprobity/config/config.php): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 24 PHP Warning: include_once(): Failed opening '/PATH/molprobity/2019/molprobity/config/config.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /PATH/molprobity/2019/molprobity/lib/core.php on line 24 Must provide at least one PDB file on the command line!

When a PDB is provided, such as with PDB 1a1x (where STUDENT_ID is my student number):

$ clashscore /users/STUDENT_ID/mol_test/1a1xA.pdb PHP Warning: include_once(/PATH/molprobity/2019/molprobity/config/config.php): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 24 PHP Warning: include_once(): Failed opening '/PATH/molprobity/2019/molprobity/config/config.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /PATH/molprobity/2019/molprobity/lib/core.php on line 24 PHP Warning: opendir(/PATH/molprobity/2019/molprobity/public_html/data): failed to open dir: No such file or directory in /PATH/molprobity/2019/molprobity/lib/sessions.php on line 328 PHP Warning: readdir() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/sessions.php on line 329 PHP Warning: closedir() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/sessions.php on line 334 PHP Warning: mkdir(): No such file or directory in /PATH/molprobity/2019/molprobity/lib/sessions.php on line 156 PHP Warning: mkdir(): No such file or directory in /PATH/molprobity/2019/molprobity/lib/sessions.php on line 157 PHP Warning: mkdir(): No such file or directory in /PATH/molprobity/2019/molprobity/lib/sessions.php on line 158 PHP Warning: mkdir(): No such file or directory in /PATH/molprobity/2019/molprobity/lib/model.php on line 161 PHP Warning: copy(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/original_uploads/1a1xA.pdb): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/model.php on line 163 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 307 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 sh: /PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/original_uploads/1a1xA.pdb: No such file or directory PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 307 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 307 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 307 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 307 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 311 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 307 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 307 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: fopen(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/system/progress): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/core.php on line 301 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fwrite() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 313 PHP Warning: fclose() expects parameter 1 to be resource, boolean given in /PATH/molprobity/2019/molprobity/lib/core.php on line 315 PHP Warning: mkdir(): No such file or directory in /PATH/molprobity/2019/molprobity/lib/model.php on line 195 PHP Warning: copy(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/coordinates/1a1xA_clean.pdb): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/model.php on line 336 PHP Warning: mkdir(): No such file or directory in /PATH/molprobity/2019/molprobity/cmdline/clashscore on line 77 sh: /PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/raw_data/1a1xA-rama.data: No such file or directory PHP Warning: file(/PATH/molprobity/2019/molprobity/public_html/data/8ium0mdri85ppcjbstr490aib0/raw_data/1a1xA-rama.data): failed to open stream: No such file or directory in /PATH/molprobity/2019/molprobity/lib/analyze.php on line 939 PHP Warning: array_slice() expects parameter 1 to be array, boolean given in /PATH/molprobity/2019/molprobity/lib/analyze.php on line 940 PHP Warning: array_values() expects parameter 1 to be array, null given in /PATH/molprobity/2019/molprobity/lib/analyze.php on line 940 PHP Warning: Invalid argument supplied for foreach() in /PATH/molprobity/2019/molprobity/lib/analyze.php on line 950

Using oneline-analysis returns similar errors and outputs this with the same PDB 1a1x (filename is 1a1xA as it's only the A chain):

pdbFileName:x-H_type:chains:residues:nucacids:resolution:rvalue:rfree:clashscore:clashscoreB<40:minresol:maxresol:n_samples:pct_rank:pct_rank40:cbeta>0.25:numCbeta:rotaOutlier:rotaFavored:numRota:ramaOutlier:ramaAllowed:ramaFavored:numRama:cisPro:totalPro:cisNonPro:totalNonPro:twistedPeptides:totalPeptides:numbadbonds:numbonds:pct_badbonds:pct_resbadbonds:numbadangles:numangles:pct_badangles:pct_resbadangles:chiralSwaps:tetraOutliers:pseudochiralErrors:cablamOutlierPct:caGeomOutlierPct:waterClashes:totalWaters:MolProbityScore:Mol_pct_rank

1a1xA.pdb:ecloud:0:0:0::::0:0:0:9999:1784:100:100:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:-1:-1:-1:-1:-1:-1:-1:-1:0:0:0:0.00:0.00:0:0::

Within the README (/molprobity/2019/molprobity/README) it says that the webserver does not need to be installed to run the command line options (/molprobity/2019/molprobity/cmdline/), is there a way to use the /cmdline/ options strictly offline without opening ports or installing webservers onto our supercomputer system please?

Reduce and Probe are working brilliantly and hopefully I can use MolProbity on our system to get MolProbity scores at some point, thank you for the code and software!

antonkulaga commented 1 year ago

same problem. Molprobity uses too antient versions