diff test-data/cut_trajectories_file.log @ 2:c574ada16e76 draft

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cut_trajectories_file.log	Wed May 25 09:42:17 2022 +0000
@@ -0,0 +1,241 @@
+INFO - verbose mode on
+INFO - Cut trajectory mode
+INFO - 
+Function search_nbr_sub_traj
+INFO - The input file is estimated_number_of_sub_trajectories.tsv
+INFO - The length of complete trajectory is 11
+INFO - The number of sub-trajectories required is  3
+INFO - The elapsed time between two steps is : 10ps
+INFO - The number of frames per sub-trajectory is 3
+INFO - End search_nbr_sub_traj function
+INFO - 
+Function cut_traj
+INFO - The length of the trajectory is 11 frames
+INFO - The elapsed time between two steps is : 10 ps
+INFO - The number of sub-trajectories required is  3
+INFO - .gro file is PIP2.1_test.gro
+INFO - .xtc file is PIP2.1_test.xtc
+INFO - Output directory is out/
+INFO - The name of .log file is log/cut_trajectories.log
+INFO - The number of cpus used is 1
+INFO - Sub_trajectory 1 starts at 0 ps and ends at 20 ps
+INFO - Sub_trajectory 2 starts at 30 ps and ends at 50 ps
+INFO - Sub_trajectory 3 starts at 60 ps and ends at 80 ps
+INFO - Launch gmx trjconv
+
+             :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
+ Christian Wennberg    Maarten Wolf      Artem Zhmurov   
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2019, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx trjconv, version 2020.1-Ubuntu-2020.1-1
+Executable:   /usr/bin/gmx
+Data prefix:  /usr
+Working dir:  /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data
+Command line:
+  gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 0 -e 20 -o out/PIP2.1_test_traj_1.xtc
+
+Will write xtc: Compressed trajectory (portable xdr format): xtc
+Group     0 (         System) has 311580 elements
+Group     1 (        Protein) has 30214 elements
+Group     2 (      Protein-H) has 14908 elements
+Group     3 (        C-alpha) has  2006 elements
+Group     4 (       Backbone) has  6018 elements
+Group     5 (      MainChain) has  8016 elements
+Group     6 (   MainChain+Cb) has  9776 elements
+Group     7 (    MainChain+H) has  9926 elements
+Group     8 (      SideChain) has 20288 elements
+Group     9 (    SideChain-H) has  6892 elements
+Group    10 (    Prot-Masses) has 30214 elements
+Group    11 (    non-Protein) has 281366 elements
+Group    12 (          Other) has 281366 elements
+Group    13 (           POPC) has 83348 elements
+Group    14 (            POT) has   176 elements
+Group    15 (            CLA) has   232 elements
+Group    16 (           TIP3) has 197610 elements
+Select a group: 
+Reading frame       0 time    0.000   
+Precision of PIP2.1_test.xtc is 0.001 (nm)
+Using output precision of 0.001 (nm)
+ ->  frame      0 time    0.000      
+
+Reading frame       1 time   10.000    ->  frame      1 time   10.000      
+
+Reading frame       2 time   20.000    ->  frame      2 time   20.000      
+
+Last frame          2 time   20.000   
+
+
+GROMACS reminds you: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in Your Family?" (Gogol Bordello)
+
+Note that major changes are planned in future for trjconv, to improve usability and utility.
+Select group for output
+Selected 0: 'System'
+             :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
+ Christian Wennberg    Maarten Wolf      Artem Zhmurov   
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2019, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx trjconv, version 2020.1-Ubuntu-2020.1-1
+Executable:   /usr/bin/gmx
+Data prefix:  /usr
+Working dir:  /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data
+Command line:
+  gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 30 -e 50 -o out/PIP2.1_test_traj_2.xtc
+
+Will write xtc: Compressed trajectory (portable xdr format): xtc
+Group     0 (         System) has 311580 elements
+Group     1 (        Protein) has 30214 elements
+Group     2 (      Protein-H) has 14908 elements
+Group     3 (        C-alpha) has  2006 elements
+Group     4 (       Backbone) has  6018 elements
+Group     5 (      MainChain) has  8016 elements
+Group     6 (   MainChain+Cb) has  9776 elements
+Group     7 (    MainChain+H) has  9926 elements
+Group     8 (      SideChain) has 20288 elements
+Group     9 (    SideChain-H) has  6892 elements
+Group    10 (    Prot-Masses) has 30214 elements
+Group    11 (    non-Protein) has 281366 elements
+Group    12 (          Other) has 281366 elements
+Group    13 (           POPC) has 83348 elements
+Group    14 (            POT) has   176 elements
+Group    15 (            CLA) has   232 elements
+Group    16 (           TIP3) has 197610 elements
+Select a group: 
+Reading frame       0 time    0.000   
+Reading frame       0 time   30.000   
+Precision of PIP2.1_test.xtc is 0.001 (nm)
+Using output precision of 0.001 (nm)
+ ->  frame      0 time   30.000      
+
+Reading frame       1 time   40.000    ->  frame      1 time   40.000      
+
+Reading frame       2 time   50.000    ->  frame      2 time   50.000      
+
+Last frame          2 time   50.000   
+
+
+GROMACS reminds you: "The use of COBOL cripples the mind; its teaching should therefore be regarded as a criminal offense." (Edsger Dijkstra)
+
+Note that major changes are planned in future for trjconv, to improve usability and utility.
+Select group for output
+Selected 0: 'System'
+             :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
+ Christian Wennberg    Maarten Wolf      Artem Zhmurov   
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2019, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx trjconv, version 2020.1-Ubuntu-2020.1-1
+Executable:   /usr/bin/gmx
+Data prefix:  /usr
+Working dir:  /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data
+Command line:
+  gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc
+
+Will write xtc: Compressed trajectory (portable xdr format): xtc
+Group     0 (         System) has 311580 elements
+Group     1 (        Protein) has 30214 elements
+Group     2 (      Protein-H) has 14908 elements
+Group     3 (        C-alpha) has  2006 elements
+Group     4 (       Backbone) has  6018 elements
+Group     5 (      MainChain) has  8016 elements
+Group     6 (   MainChain+Cb) has  9776 elements
+Group     7 (    MainChain+H) has  9926 elements
+Group     8 (      SideChain) has 20288 elements
+Group     9 (    SideChain-H) has  6892 elements
+Group    10 (    Prot-Masses) has 30214 elements
+Group    11 (    non-Protein) has 281366 elements
+Group    12 (          Other) has 281366 elements
+Group    13 (           POPC) has 83348 elements
+Group    14 (            POT) has   176 elements
+Group    15 (            CLA) has   232 elements
+Group    16 (           TIP3) has 197610 elements
+Select a group: 
+Reading frame       0 time    0.000   
+Reading frame       0 time   60.000   
+Precision of PIP2.1_test.xtc is 0.001 (nm)
+Using output precision of 0.001 (nm)
+ ->  frame      0 time   60.000      
+
+Reading frame       1 time   70.000    ->  frame      1 time   70.000      
+
+Reading frame       2 time   80.000    ->  frame      2 time   80.000      
+
+Last frame          2 time   80.000   
+
+
+GROMACS reminds you: "C++ is tricky. You can do everything. You can even make every mistake." (Nicolai Josuttis, CppCon2017)
+
+Note that major changes are planned in future for trjconv, to improve usability and utility.
+Select group for output
+Selected 0: 'System'
+INFO - End cut_traj function