search

rlabduke / MolProbity

Protein and nucleic acid validation service
Other
56 stars 30 forks source link

The initial run after installation failed #29

Closed zongyangdu closed 7 months ago

zongyangdu commented 7 months ago

Hi MolProbity team! I am encountering an issue while running MolProbity using the simple_molprobity.sh script. The error messages I receive are as follows:

./simple_molprobity.sh: line 240: mmtbx.mp_geo: command not found ./simple_molprobity.sh: line 253: phenix.clashscore: command not found ./simple_molprobity.sh: line 233: phenix.suitename: command not found ....

Does this mean my installation was not successful? Do you have any solution for the above issues?

chrissciwilliams commented 7 months ago

Thanks for using MolProbity!

We recently made changes to our installers, and there was a week or so when the installation didn't work properly. That is the most likely cause.

You can check this by looking for the location of the molprobity directory (lower-case m, contains public_html). If molprobity is inside modules, then you got the weird installation. If molprobity is next to modules, then the problem is something else.

I recommend starting a fresh installation, now that the changes have been resolved. If the problem persists, let me know and we'll dig deeper.

Good luck, -Christopher Williams ---Richardson Lab, Duke University

On Thu, Dec 7, 2023 at 6:36 AM zongyangdu @.***> wrote:

Hi MolProbity team! I am encountering an issue while running MolProbity using the simple_molprobity.sh script. The error messages I receive are as follows:

./simple_molprobity.sh: line 240: mmtbx.mp_geo: command not found ./simple_molprobity.sh: line 253: phenix.clashscore: command not found ./simple_molprobity.sh: line 233: phenix.suitename: command not found ....

Does this mean my installation was not successful? Do you have any solution for the above issues?

— Reply to this email directly, view it on GitHub https://github.com/rlabduke/MolProbity/issues/29, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLEREAWC2CI6I33JESWDATYIGS3NAVCNFSM6AAAAABAK5BOCSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTANJXGMZDGOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

zongyangdu commented 7 months ago

Thanks for using MolProbity! We recently made changes to our installers, and there was a week or so when the installation didn't work properly. That is the most likely cause. You can check this by looking for the location of the molprobity directory (lower-case m, contains public_html). If molprobity is inside modules, then you got the weird installation. If molprobity is next to modules, then the problem is something else. I recommend starting a fresh installation, now that the changes have been resolved. If the problem persists, let me know and we'll dig deeper. Good luck, -Christopher Williams ---Richardson Lab, Duke University … On Thu, Dec 7, 2023 at 6:36 AM zongyangdu @.> wrote: Hi MolProbity team! I am encountering an issue while running MolProbity using the simple_molprobity.sh script. The error messages I receive are as follows: ./simple_molprobity.sh: line 240: mmtbx.mp_geo: command not found ./simple_molprobity.sh: line 253: phenix.clashscore: command not found ./simple_molprobity.sh: line 233: phenix.suitename: command not found .... Does this mean my installation was not successful? Do you have any solution for the above issues? — Reply to this email directly, view it on GitHub <#29>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLEREAWC2CI6I33JESWDATYIGS3NAVCNFSM6AAAAABAK5BOCSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTANJXGMZDGOA . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you for your response. I downloaded the latest version of MolProbity yesterday, but I couldn't find the molprobity folder you mentioned after installation. Here is the check_config.html after running setup.sh:

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

MolProbity - check configuration
[ PHP info | Configuration check | Live sessions | Usage history ]

Server information:

Directories on your PATH:

External programs required by MolProbity:

Version numbers for external programs:

chrissciwilliams commented 7 months ago

Hmm. The setup.sh script you ran is in the molprobity folder I was asking about. So you definitely have that . . .

Did you perhaps simply clone the molprobity repository? The intended way to install MolProbity is to download the "install_via_bootstrap.sh" script and run that. It will clone the molprobity repository and also install all the Phenix/cctbx stuff that seems to be missing for you.

These instructions are in the readme, but I recommend: mkdir MolProbity

cd MolProbity

wget -O install_via_bootstrap.sh https://github.com/rlabduke/MolProbity/raw/master/install_via_bootstrap.sh

bash install_via_bootstrap.sh 4

cd molprobity

bash setup.sh

Good luck, -Christopher Williams ---Richardson Lab, Duke University

On Thu, Dec 7, 2023 at 10:15 PM zongyangdu @.***> wrote:

Thanks for using MolProbity! We recently made changes to our installers, and there was a week or so when the installation didn't work properly. That is the most likely cause. You can check this by looking for the location of the molprobity directory (lower-case m, contains public_html). If molprobity is

inside modules, then you got the weird installation. If molprobity is next to modules, then the problem is something else. I recommend starting a fresh installation, now that the changes have been resolved. If the problem persists, let me know and we'll dig deeper. Good luck, -Christopher Williams ---Richardson Lab, Duke University … <#m-3667049376002451149> On Thu, Dec 7, 2023 at 6:36 AM zongyangdu @.> wrote: Hi MolProbity team! I am encountering an issue while running MolProbity using the simple_molprobity.sh script. The error messages I receive are as follows: ./simple_molprobity.sh: line 240: mmtbx.mp_geo: command not found ./simple_molprobity.sh: line 253: phenix.clashscore: command not found ./simple_molprobity.sh: line 233: phenix.suitename: command not found .... Does this mean my installation was not successful? Do you have any solution for the above issues? — Reply to this email directly, view it on GitHub <#29 https://github.com/rlabduke/MolProbity/issues/29>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLEREAWC2CI6I33JESWDATYIGS3NAVCNFSM6AAAAABAK5BOCSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTANJXGMZDGOA https://github.com/notifications/unsubscribe-auth/ACLEREAWC2CI6I33JESWDATYIGS3NAVCNFSM6AAAAABAK5BOCSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTANJXGMZDGOA . You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you for your response. I downloaded the latest version of MolProbity yesterday, but I couldn't find the molprobity folder you mentioned after installation. Here is the check_config.html after running setup.sh:

MolProbity - check configuration [ PHP info | Configuration check | Live sessions | Usage history ] ------------------------------ Server information: - Current URL: http://public_html/admin/check_config.php - Operating system: Linux - PHP version (webserver): 5.6.40-68+ubuntu20.04.1+deb.sury.org+1 - fine. - *PHP version (cmd line): PHP 5.6.40-68+ubuntu20.04.1+deb.sury.org +1 (cli) * - warning: does not match webserver version (5.6.40-68+ubuntu20.04.1+deb.sury.org+1). - CLI version of PHP installed - good. - File uploads are enabled - good. Maximum size for file uploads will be the *minimum* of: - post_max_size: *8M* (in /etc/php.ini or equivalent) - upload_max_filesize: *2M* (in /etc/php.ini or equivalent) - ...and any LimitRequestBody directives in /etc/httpd/httpd.conf (for Apache web server, anyway). - URL fopen wrappers are allowed - good. - Safe mode disabled - good. - Magic quotes GPC is disabled - good. - *PHP display_errors is disabled.* This makes it much harder to debug MolProbity, so check your webserver logs for PHP errors. ------------------------------ Directories on your PATH: - */usr/local/php5/bin - does not exist* - */opt/j2/bin - does not exist* - */usr/java/jdk/bin - does not exist* - /data1/duzy/software/MolProbity/bin - /data1/duzy/software/MolProbity/bin/linux - */usr/local/php5/bin - does not exist* - */opt/j2/bin - does not exist* - */usr/java/jdk/bin - does not exist* - /data1/duzy/software/MolProbity/build/bin - */usr/local/php5/bin - does not exist* - */opt/j2/bin - does not exist* - */usr/java/jdk/bin - does not exist* - /data1/duzy/software/MolProbity/bin - /data1/duzy/software/MolProbity/bin/linux - /home/duzy/bin - /data1/duzy/software/apache-maven-3.9.6/bin - /data1/duzy/software/hh-suite/build/bin - /data1/duzy/software/hh-suite/build/scripts - /data1/duzy/software/cplex/cplex/bin/x86-64_linux - /data1/duzy/software/cplex/cpoptimizer/bin/x86-64_linux - /data1/duzy/software/RNAView-master/bin - /home/duzy/miniconda3/bin - /home/duzy/miniconda3/condabin - /usr/local/sbin - /usr/local/bin - /usr/sbin - /usr/bin - /sbin - /bin - /usr/games - /usr/local/games - /snap/bin ------------------------------ External programs required by MolProbity: - which: /usr/bin/which - rm: /usr/bin/rm - du: /usr/bin/du - df: /usr/bin/df - fold: /usr/bin/fold - zip: /usr/bin/zip - gzip: /usr/bin/gzip - gunzip: /usr/bin/gunzip - php: /usr/bin/php - awk: /usr/bin/awk - gawk: /data1/duzy/software/MolProbity/bin/linux/gawk - perl: /home/duzy/miniconda3/bin/perl - java: /usr/bin/java - reduce: /data1/duzy/software/MolProbity/bin/linux/reduce - prekin: /data1/duzy/software/MolProbity/bin/linux/prekin - probe: /data1/duzy/software/MolProbity/bin/linux/probe - flipkin: /data1/duzy/software/MolProbity/bin/flipkin - clashlist: /data1/duzy/software/MolProbity/bin/clashlist - cluster: /data1/duzy/software/MolProbity/bin/linux/cluster - suitename: /data1/duzy/software/MolProbity/bin/linux/suitename - pdbcns: /data1/duzy/software/MolProbity/bin/pdbcns - dang: /data1/duzy/software/MolProbity/bin/linux/dang - scrublines: /data1/duzy/software/MolProbity/bin/linux/scrublines - cksegid.pl: /data1/duzy/software/MolProbity/bin/cksegid.pl - sswing: /data1/duzy/software/MolProbity/bin/sswing - sswingmkrotscrByPerl: /data1/duzy/software/MolProbity/bin/sswingmkrotscrByPerl - sswingpdb2rotscr: /data1/duzy/software/MolProbity/bin/sswingpdb2rotscr - genContour: /data1/duzy/software/MolProbity/bin/linux/genContour - genScoreResult: /data1/duzy/software/MolProbity/bin/linux/genScoreResult - preGenScore: /data1/duzy/software/MolProbity/bin/linux/preGenScore - noe-display: /data1/duzy/software/MolProbity/bin/linux/noe-display ------------------------------ Version numbers for external programs: - Java (cmd line): openjdk version "11.0.21" 2023-10-17 - Prekin: PREKIN version 6.57, Linux, dated: 130508 NOGUI - Reduce: reduce: version 3.24 07/24/2013, Copyright 1997-2013, J. Michael Word - Probe: probe.2.16.130520 - NOE-display: Version 0.5.8.005, 19 May 2004 (ALPHA) — Reply to this email directly, view it on GitHub , or unsubscribe . You are receiving this because you commented.Message ID: ***@***.***>
zongyangdu commented 7 months ago

Hmm. The setup.sh script you ran is in the molprobity folder I was asking about. So you definitely have that . . . Did you perhaps simply clone the molprobity repository? The intended way to install MolProbity is to download the "install_via_bootstrap.sh" script and run that. It will clone the molprobity repository and also install all the Phenix/cctbx stuff that seems to be missing for you. These instructions are in the readme, but I recommend: mkdir MolProbity cd MolProbity wget -O install_via_bootstrap.sh https://github.com/rlabduke/MolProbity/raw/master/install_via_bootstrap.sh bash install_via_bootstrap.sh 4 cd molprobity bash setup.sh Good luck, -Christopher Williams ---Richardson Lab, Duke University … On Thu, Dec 7, 2023 at 10:15 PM zongyangdu @.> wrote: Thanks for using MolProbity! We recently made changes to our installers, and there was a week or so when the installation didn't work properly. That is the most likely cause. You can check this by looking for the location of the molprobity directory (lower-case m, contains public_html). If molprobity is inside modules, then you got the weird installation. If molprobity is next to modules, then the problem is something else. I recommend starting a fresh installation, now that the changes have been resolved. If the problem persists, let me know and we'll dig deeper. Good luck, -Christopher Williams ---Richardson Lab, Duke University … <#m-3667049376002451149> On Thu, Dec 7, 2023 at 6:36 AM zongyangdu @.> wrote: Hi MolProbity team! I am encountering an issue while running MolProbity using the simple_molprobity.sh script. The error messages I receive are as follows: ./simple_molprobity.sh: line 240: mmtbx.mp_geo: command not found ./simple_molprobity.sh: line 253: phenix.clashscore: command not found ./simple_molprobity.sh: line 233: phenix.suitename: command not found .... Does this mean my installation was not successful? Do you have any solution for the above issues? — Reply to this email directly, view it on GitHub <#29 <#29>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLEREAWC2CI6I33JESWDATYIGS3NAVCNFSM6AAAAABAK5BOCSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTANJXGMZDGOA https://github.com/notifications/unsubscribe-auth/ACLEREAWC2CI6I33JESWDATYIGS3NAVCNFSM6AAAAABAK5BOCSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZTANJXGMZDGOA . You are receiving this because you are subscribed to this thread.Message ID: @.> Thank you for your response. I downloaded the latest version of MolProbity yesterday, but I couldn't find the molprobity folder you mentioned after installation. Here is the check_config.html after running setup.sh: MolProbity - check configuration [ PHP info http://phpinfo.php | Configuration check http://check_config.php | Live sessions http://show_sessions.php | Usage history http://usage_history.php ] ------------------------------ Server information: - Current URL: http://public_html/admin/check_config.php - Operating system: Linux - PHP version (webserver): 5.6.40-68+ubuntu20.04.1+deb.sury.org+1 - fine. - PHP version (cmd line): PHP 5.6.40-68+ubuntu20.04.1+deb.sury.org http://deb.sury.org+1 (cli) - warning: does not match webserver version (5.6.40-68+ubuntu20.04.1+deb.sury.org+1). - CLI version of PHP installed - good. - File uploads are enabled - good. Maximum size for file uploads will be the minimum of: - post_max_size: 8M (in /etc/php.ini or equivalent) - upload_max_filesize: 2M (in /etc/php.ini or equivalent) - ...and any LimitRequestBody directives in /etc/httpd/httpd.conf (for Apache web server, anyway). - URL fopen wrappers are allowed - good. - Safe mode disabled - good. - Magic quotes GPC is disabled - good. - PHP display_errors is disabled. This makes it much harder to debug MolProbity, so check your webserver logs for PHP errors. ------------------------------ Directories on your PATH: - /usr/local/php5/bin - does not exist - /opt/j2/bin - does not exist - /usr/java/jdk/bin - does not exist - /data1/duzy/software/MolProbity/bin - /data1/duzy/software/MolProbity/bin/linux - /usr/local/php5/bin - does not exist - /opt/j2/bin - does not exist - /usr/java/jdk/bin - does not exist - /data1/duzy/software/MolProbity/build/bin - /usr/local/php5/bin - does not exist - /opt/j2/bin - does not exist - /usr/java/jdk/bin - does not exist - /data1/duzy/software/MolProbity/bin - /data1/duzy/software/MolProbity/bin/linux - /home/duzy/bin - /data1/duzy/software/apache-maven-3.9.6/bin - /data1/duzy/software/hh-suite/build/bin - /data1/duzy/software/hh-suite/build/scripts - /data1/duzy/software/cplex/cplex/bin/x86-64_linux - /data1/duzy/software/cplex/cpoptimizer/bin/x86-64_linux - /data1/duzy/software/RNAView-master/bin - /home/duzy/miniconda3/bin - /home/duzy/miniconda3/condabin - /usr/local/sbin - /usr/local/bin - /usr/sbin - /usr/bin - /sbin - /bin - /usr/games - /usr/local/games - /snap/bin ------------------------------ External programs required by MolProbity: - which: /usr/bin/which - rm: /usr/bin/rm - du: /usr/bin/du - df: /usr/bin/df - fold: /usr/bin/fold - zip: /usr/bin/zip - gzip: /usr/bin/gzip - gunzip: /usr/bin/gunzip - php: /usr/bin/php - awk: /usr/bin/awk - gawk: /data1/duzy/software/MolProbity/bin/linux/gawk - perl: /home/duzy/miniconda3/bin/perl - java: /usr/bin/java - reduce: /data1/duzy/software/MolProbity/bin/linux/reduce - prekin: /data1/duzy/software/MolProbity/bin/linux/prekin - probe: /data1/duzy/software/MolProbity/bin/linux/probe - flipkin: /data1/duzy/software/MolProbity/bin/flipkin - clashlist: /data1/duzy/software/MolProbity/bin/clashlist - cluster: /data1/duzy/software/MolProbity/bin/linux/cluster - suitename: /data1/duzy/software/MolProbity/bin/linux/suitename - pdbcns: /data1/duzy/software/MolProbity/bin/pdbcns - dang: /data1/duzy/software/MolProbity/bin/linux/dang - scrublines: /data1/duzy/software/MolProbity/bin/linux/scrublines - cksegid.pl: /data1/duzy/software/MolProbity/bin/cksegid.pl - sswing: /data1/duzy/software/MolProbity/bin/sswing - sswingmkrotscrByPerl: /data1/duzy/software/MolProbity/bin/sswingmkrotscrByPerl - sswingpdb2rotscr: /data1/duzy/software/MolProbity/bin/sswingpdb2rotscr - genContour: /data1/duzy/software/MolProbity/bin/linux/genContour - genScoreResult: /data1/duzy/software/MolProbity/bin/linux/genScoreResult - preGenScore: /data1/duzy/software/MolProbity/bin/linux/preGenScore - noe-display: /data1/duzy/software/MolProbity/bin/linux/noe-display ------------------------------ Version numbers for external programs: - Java (cmd line): openjdk version "11.0.21" 2023-10-17 - Prekin: PREKIN version 6.57, Linux, dated: 130508 NOGUI - Reduce: reduce: version 3.24 07/24/2013, Copyright 1997-2013, J. Michael Word - Probe: probe.2.16.130520 - NOE-display: Version 0.5.8.005, 19 May 2004 (ALPHA) — Reply to this email directly, view it on GitHub <#29 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLEREFZAOLM3IVEOQ3H5MTYIKA3NAVCNFSM6AAAAABAK5BOCSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBWGQ4DOOBXGU . You are receiving this because you commented.Message ID: @.>

I found that the line 'python boostrap.py ...' in the shell script wasn't executed, and there were no error messages during the last installation. Now, MolProbity runs successfully. Thank you very much for your help!