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Error: dials.export subprocess failed with exitcode 1 #2631

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mysecondnameisdanger opened this issue Mar 17, 2024 · 4 comments
Open

Error: dials.export subprocess failed with exitcode 1 #2631

mysecondnameisdanger opened this issue Mar 17, 2024 · 4 comments

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@mysecondnameisdanger
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mysecondnameisdanger commented Mar 17, 2024 •
edited

I was experimenting... I put all datasets in a single folder and tried to run dials ... and got this. I guess the datasets are too different and cannot be merged...?
This is a single crystal, 10 datasets, and for each dataset there are 2 sweeps 45 degrees apart ( I think..).

msnid@fedora:~$ xia2 space_group=P43212 /home/msnid/raw_data/B3X11/all/
Environment configuration...
Python => /home/msnid/xstl/dials-v3-18-0/build/../conda_base/bin/python
CCTBX => /home/msnid/xstl/dials-v3-18-0/modules
CCP4 => /home/msnid/xstl/ccp4-8.0
CCP4_SCR => /tmp/tmpfnssosm_
Starting directory: /home/msnid
Working directory: /home/msnid
Free space:        115.97 GB
Host: fedora
Contact: xia2.support@gmail.com
XIA2 3.18.0
DIALS 3.18.0-gbecf27540-release
CCP4 8.0.017
Warning: Ambiguous parameter definition: space_group = P43212
Best matches:
  dials.masking.ice_rings.space_group
  xia2.settings.space_group
  xia2.settings.resolution.space_group
Assuming xia2.settings.space_group was intended.
Command line: xia2 space_group=P43212 /home/msnid/raw_data/B3X11/all/
Project directory: /home/msnid
-------------------- Spotfinding SWEEP1 --------------------
91470 spots found on 90 images (max 2165 / bin)
*                                                          *
*                                                          *
*              ******** ****         *                     *
* **   ******* ************************** *      *        **
******************************************** ***************
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP1 --------------------
All possible indexing solutions:
tP  78.60  78.60  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.60  78.60  36.97  90.00  90.00  90.00
-------------------- Integrating SWEEP1 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.26 0.35
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.149 < 0.149 < 0.149
-------------------- Spotfinding SWEEP2 --------------------
80473 spots found on 90 images (max 2163 / bin)
*                                                           
*                                                           
*                                                          *
*                                      *                   *
************** ***************************** ***************
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP2 --------------------
All possible indexing solutions:
tP  78.79  78.79  37.00  90.00  90.00  90.00
Indexing solution:
tP  78.79  78.79  37.00  90.00  90.00  90.00
-------------------- Integrating SWEEP2 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.51 0.60
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.129 < 0.129 < 0.129
-------------------- Spotfinding SWEEP3 --------------------
85924 spots found on 90 images (max 2068 / bin)
*                                                          *
*                                                          *
*               ******** **           *                    *
**** *  ****** *************************** *  *            *
******************************************** ***************
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP3 --------------------
All possible indexing solutions:
tP  78.61  78.61  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.61  78.61  36.97  90.00  90.00  90.00
-------------------- Integrating SWEEP3 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.27 0.37
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.156 < 0.156 < 0.156
-------------------- Spotfinding SWEEP4 --------------------
77519 spots found on 90 images (max 2242 / bin)
*                                                           
*                                                           
*                                                          *
*                                                          *
*** ******** * ***   **  *** *************** * ** ** *   ***
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP4 --------------------
All possible indexing solutions:
tP  78.81  78.81  37.01  90.00  90.00  90.00
Indexing solution:
tP  78.81  78.81  37.01  90.00  90.00  90.00
-------------------- Integrating SWEEP4 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.48 0.55
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.125 < 0.125 < 0.125
-------------------- Spotfinding SWEEP5 --------------------
82034 spots found on 90 images (max 1979 / bin)
*                                                           
*                                                          *
*               *******  *                                 *
******   ***** ************************* *                 *
******************************************** ***************
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP5 --------------------
All possible indexing solutions:
tP  78.61  78.61  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.61  78.61  36.97  90.00  90.00  90.00
-------------------- Integrating SWEEP5 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.27 0.39
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.155 < 0.155 < 0.155
-------------------- Spotfinding SWEEP6 --------------------
74502 spots found on 90 images (max 2133 / bin)
*                                                           
*                                                           
*                                                           
*                                                          *
************** **** **** ******************* ****** *     **
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP6 --------------------
All possible indexing solutions:
tP  78.83  78.83  37.03  90.00  90.00  90.00
Indexing solution:
tP  78.83  78.83  37.03  90.00  90.00  90.00
-------------------- Integrating SWEEP6 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.45 0.55
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.124 < 0.124 < 0.124
-------------------- Spotfinding SWEEP7 --------------------
80705 spots found on 90 images (max 1987 / bin)
*                                                          *
*                                                          *
*               ******* * *                                *
**       ***** ***************************                 *
******************************************** ***************
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP7 --------------------
All possible indexing solutions:
tP  78.62  78.62  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.62  78.62  36.97  90.00  90.00  90.00
-------------------- Integrating SWEEP7 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.28 0.38
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.156 < 0.156 < 0.156
-------------------- Spotfinding SWEEP8 --------------------
72270 spots found on 90 images (max 2182 / bin)
*                                                           
*                                                           
*                                                           
*                                                          *
********   *** ***   **   ** ** ****** ** ** *             *
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP8 --------------------
All possible indexing solutions:
tP  78.85  78.85  37.03  90.00  90.00  90.00
Indexing solution:
tP  78.85  78.85  37.03  90.00  90.00  90.00
-------------------- Integrating SWEEP8 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.43 0.53
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.126 < 0.126 < 0.126
-------------------- Spotfinding SWEEP9 --------------------
79862 spots found on 90 images (max 1984 / bin)
*                                                          *
*                                                          *
*               * ******* *                                *
**        **** ****************** ****** **                *
******************************************** ************ **
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP9 --------------------
All possible indexing solutions:
tP  78.63  78.63  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.63  78.63  36.97  90.00  90.00  90.00
-------------------- Integrating SWEEP9 --------------------
 Processed batches 2 to 91
Standard Deviation in pixel range: 0.28 0.40
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.148 < 0.148 < 0.148
------------------- Spotfinding SWEEP10 --------------------
70131 spots found on 90 images (max 2192 / bin)
*                                                           
*                                                           
*                                                           
*                                                          *
*  ******  *     *     *        ***                        *
******************************************************   * *
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP10 -------------------
All possible indexing solutions:
tP  78.87  78.87  37.05  90.00  90.00  90.00
Indexing solution:
tP  78.87  78.87  37.05  90.00  90.00  90.00
------------------- Integrating SWEEP10 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.43 0.52
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.122 < 0.122 < 0.122
------------------- Spotfinding SWEEP11 --------------------
78576 spots found on 90 images (max 2033 / bin)
*                                                           
*                                                           
*                   * *                                    *
*         * *  **************** *** ****                   *
************** ***************************** ******** *    *
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP11 -------------------
All possible indexing solutions:
tP  78.63  78.63  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.63  78.63  36.97  90.00  90.00  90.00
------------------- Integrating SWEEP11 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.28 0.43
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.146 < 0.146 < 0.146
------------------- Spotfinding SWEEP12 --------------------
67422 spots found on 90 images (max 2105 / bin)
*                                                           
*                                                           
*                                                           
*                                                          *
* ******     *  **        **  *  ** *  *                   *
******************************************** *********     *
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP12 -------------------
All possible indexing solutions:
tP  78.88  78.88  37.05  90.00  90.00  90.00
Indexing solution:
tP  78.88  78.88  37.05  90.00  90.00  90.00
------------------- Integrating SWEEP12 --------------------
 Processed batches 182 to 271
Standard Deviation in pixel range: 0.42 0.53
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.125 < 0.125 < 0.125
------------------- Spotfinding SWEEP13 --------------------
76810 spots found on 90 images (max 1884 / bin)
*                                                           
*                                                           
*                 ******* **                               *
***** *  ***** *************************** * *   *         *
******************************************** ********** *  *
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP13 -------------------
All possible indexing solutions:
tP  78.63  78.63  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.63  78.63  36.97  90.00  90.00  90.00
------------------- Integrating SWEEP13 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.28 0.44
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.155 < 0.155 < 0.155
------------------- Spotfinding SWEEP14 --------------------
65139 spots found on 90 images (max 2062 / bin)
*                                                           
*                                                           
*                                                           
*                                                           
** *****     * * *            *   **   *     *             *
************** ***************************** ******        *
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP14 -------------------
All possible indexing solutions:
tP  78.90  78.90  37.06  90.00  90.00  90.00
Indexing solution:
tP  78.90  78.90  37.06  90.00  90.00  90.00
------------------- Integrating SWEEP14 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.43 0.52
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.120 < 0.120 < 0.120
------------------- Spotfinding SWEEP15 --------------------
75042 spots found on 90 images (max 1891 / bin)
*                                                           
*                                                           
*                  * **   *                                *
** *      * ** ****************** ******** *               *
******************************************** **********    *
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP15 -------------------
All possible indexing solutions:
tP  78.64  78.64  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.64  78.64  36.97  90.00  90.00  90.00
------------------- Integrating SWEEP15 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.29 0.49
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.149 < 0.149 < 0.149
------------------- Spotfinding SWEEP16 --------------------
62601 spots found on 90 images (max 2029 / bin)
*                                                           
*                                                           
*                                                           
*                                                           
** ** **     *   *               *                         *
******************************************** *** ***       *
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP16 -------------------
All possible indexing solutions:
tP  78.91  78.91  37.05  90.00  90.00  90.00
Indexing solution:
tP  78.91  78.91  37.05  90.00  90.00  90.00
------------------- Integrating SWEEP16 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.43 0.52
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.121 < 0.121 < 0.121
------------------- Spotfinding SWEEP17 --------------------
72318 spots found on 90 images (max 1881 / bin)
*                                                           
*                                                           
*                   **                                      
** **        * *************** * ** *****                  *
******************************************** ********      *
*********************************************************  *
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP17 -------------------
All possible indexing solutions:
tP  78.65  78.65  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.65  78.65  36.97  90.00  90.00  90.00
------------------- Integrating SWEEP17 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.29 0.52
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.156 < 0.156 < 0.156
------------------- Spotfinding SWEEP18 --------------------
60593 spots found on 90 images (max 1947 / bin)
*                                                           
*                                                           
*                                                           
*                                                           
** *****     *                   *                         *
******************************************** ** ***        *
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP18 -------------------
All possible indexing solutions:
tP  78.94  78.94  37.06  90.00  90.00  90.00
Indexing solution:
tP  78.94  78.94  37.06  90.00  90.00  90.00
------------------- Integrating SWEEP18 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.43 0.51
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.124 < 0.124 < 0.124
------------------- Spotfinding SWEEP19 --------------------
70939 spots found on 90 images (max 1849 / bin)
*                                                           
*                                                           
*                   **** *                                  
** *         *  *******************  *** *                  
************** ***************************** ******        *
*********************************************************  *
************************************************************
************************************************************
************************************************************
************************************************************
1                          image                          90
------------------- Autoindexing SWEEP19 -------------------
All possible indexing solutions:
tP  78.66  78.66  36.97  90.00  90.00  90.00
Indexing solution:
tP  78.66  78.66  36.97  90.00  90.00  90.00
------------------- Integrating SWEEP19 --------------------
Processed batches 2 to 91
Standard Deviation in pixel range: 0.29 0.53
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.152 < 0.152 < 0.152
------------------- Spotfinding SWEEP20 --------------------
58990 spots found on 90 images (max 1965 / bin)
*                                                           
*                                                           
*                                                           
*                                                           
*  ** **                   *                               *
************** ***************************** **   *        *
************************************************************
************************************************************
************************************************************
************************************************************
181                        image                         270
------------------- Autoindexing SWEEP20 -------------------
All possible indexing solutions:
tP  78.95  78.95  37.08  90.00  90.00  90.00
Indexing solution:
tP  78.95  78.95  37.08  90.00  90.00  90.00
------------------- Integrating SWEEP20 --------------------
Processed batches 182 to 271
Standard Deviation in pixel range: 0.42 0.53
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.123 < 0.123 < 0.123
-------------------- Preparing DEFAULT ---------------------
Reindexing all datasets to common reference
--------------------- Scaling DEFAULT ----------------------
Resolution for sweep NATIVE/SWEEP1: 1.00 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP2: 0.00
Resolution for sweep NATIVE/SWEEP3: 0.00
Resolution for sweep NATIVE/SWEEP4: 0.00
Resolution for sweep NATIVE/SWEEP5: 0.00
Resolution for sweep NATIVE/SWEEP6: 0.00
Resolution for sweep NATIVE/SWEEP7: 0.00
Resolution for sweep NATIVE/SWEEP8: 1.01 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP9: 1.00 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP10: 1.02 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP11: 1.00 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP12: 1.03 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP13: 1.02 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP14: 1.05 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP15: 1.01 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP16: 1.07 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP17: 1.03 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP18: 1.08 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP19: 1.03 (cc_half > 0.3)
Resolution for sweep NATIVE/SWEEP20: 1.10 (cc_half > 0.3)
--------------------- Scaling DEFAULT ----------------------
------------------- Unit cell refinement -------------------
Overall:  78.85  78.85  36.94  90.00  90.00  90.00
Error: dials.export subprocess failed with exitcode 1: see /home/msnid/DEFAULT/scale/283_dials.export.log for more details
Please send the contents of xia2.txt, xia2-error.txt and xia2-debug.txt to:
xia2.support@gmail.com
msnid@fedora:~$   cat /home/msnid/DEFAULT/scale/283_dials.export.log
DIALS (2018) Acta Cryst. D74, 85-97. https://doi.org/10.1107/S2059798317017235
DIALS 3.18.0-gbecf27540-release
The following parameters have been modified:

intensity = auto profile sum *scale
mtz {
  hklout = "/home/msnid/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_unmerged.mtz"
  crystal_name = "DEFAULT"
  project_name = "AUTOMATIC"
}
input {
  experiments = /home/msnid/DEFAULT/scale/282_refined_cell.expt
  reflections = /home/msnid/DEFAULT/scale/281_scaled.refl
}

--------------------------------------------------------------------------------
  template: /home/msnid/raw_data/B3X11/all/B3X11_09_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_03_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_07_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_06_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_05_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_06_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_07_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_05_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_10_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_02_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_04_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_01_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_09_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_03_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_02_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_08_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_04_####.cbf.bz2:181:270
  template: /home/msnid/raw_data/B3X11/all/B3X11_10_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_08_####.cbf.bz2:1:90
  template: /home/msnid/raw_data/B3X11/all/B3X11_01_####.cbf.bz2:1:90
--------------------------------------------------------------------------------
Experiment crystals differ. Using first experiment crystal for file-level data.
Using median unit cell across experiments : (78.8543, 78.8543, 36.9411, 90, 90, 90)
Read 3293034 predicted reflections
Selected 2945287 scaled reflections
Removed 0 intensity.scale.value reflections with I/Sig(I) < -5.0
Error: Duplicate batch offsets detected: 0, 180
# command line:
# dials.export  'experiments=282_refined_cell.expt' 'reflections=281_scaled.refl' 'mtz.hklout=AUTOMATIC_DEFAULT_scaled_unmerged.mtz' 'mtz.crystal_name=DEFAULT' 'mtz.project_name=AUTOMATIC' 'combine_partials=true' 'partiality_threshold=0.4' 'intensity=scale'
#
# timing information:
#   time since object initialization: 18.8 seconds
#   time since process start: 18.8 seconds
msnid@fedora:~$ cat xia2-error.txt 
Traceback (most recent call last):
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/cli/xia2_main.py", line 331, in run
    xia2_main()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/cli/xia2_main.py", line 264, in xia2_main
    logger.info(xinfo.get_output())
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Schema/XProject.py", line 120, in get_output
    result += self._crystals[crystal].get_output()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Schema/XCrystal.py", line 360, in get_output
    reflections_all = self.get_scaled_merged_reflections()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Schema/XCrystal.py", line 738, in get_scaled_merged_reflections
    return self._get_scaler().get_scaled_merged_reflections()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Schema/Interfaces/Scaler.py", line 397, in get_scaled_merged_reflections
    self.scale()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Schema/Interfaces/Scaler.py", line 373, in scale
    self._scalr_result = self._scale()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Modules/Scaler/DialsScaler.py", line 844, in _scale
    exporter.run()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Wrappers/Dials/ExportMtz.py", line 75, in run
    self.check_for_errors()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Driver/DefaultDriver.py", line 253, in check_for_errors
    self.check_return_code()
  File "/home/msnid/xstl/dials-v3-18-0/modules/xia2/src/xia2/Driver/DefaultDriver.py", line 300, in check_return_code
    raise RuntimeError(
RuntimeError: dials.export subprocess failed with exitcode 1: see /home/msnid/DEFAULT/scale/283_dials.export.log for more details
msnid@fedora:~$ ls -1 raw_data/B3X11/all/
B3X11_01_0001.cbf.bz2
B3X11_01_0002.cbf.bz2
B3X11_01_0003.cbf.bz2
B3X11_01_0004.cbf.bz2
B3X11_01_0005.cbf.bz2
B3X11_01_0006.cbf.bz2
B3X11_01_0007.cbf.bz2
B3X11_01_0008.cbf.bz2
B3X11_01_0009.cbf.bz2
B3X11_01_0010.cbf.bz2
B3X11_01_0011.cbf.bz2
B3X11_01_0012.cbf.bz2
B3X11_01_0013.cbf.bz2
B3X11_01_0014.cbf.bz2
B3X11_01_0015.cbf.bz2
B3X11_01_0016.cbf.bz2
B3X11_01_0017.cbf.bz2
B3X11_01_0018.cbf.bz2
B3X11_01_0019.cbf.bz2
B3X11_01_0020.cbf.bz2
B3X11_01_0021.cbf.bz2
B3X11_01_0022.cbf.bz2
B3X11_01_0023.cbf.bz2
B3X11_01_0024.cbf.bz2
B3X11_01_0025.cbf.bz2
B3X11_01_0026.cbf.bz2
B3X11_01_0027.cbf.bz2
B3X11_01_0028.cbf.bz2
B3X11_01_0029.cbf.bz2
B3X11_01_0030.cbf.bz2
B3X11_01_0031.cbf.bz2
B3X11_01_0032.cbf.bz2
B3X11_01_0033.cbf.bz2
B3X11_01_0034.cbf.bz2
B3X11_01_0035.cbf.bz2
B3X11_01_0036.cbf.bz2
B3X11_01_0037.cbf.bz2
B3X11_01_0038.cbf.bz2
B3X11_01_0039.cbf.bz2
B3X11_01_0040.cbf.bz2
B3X11_01_0041.cbf.bz2
B3X11_01_0042.cbf.bz2
B3X11_01_0043.cbf.bz2
B3X11_01_0044.cbf.bz2
B3X11_01_0045.cbf.bz2
B3X11_01_0046.cbf.bz2
B3X11_01_0047.cbf.bz2
B3X11_01_0048.cbf.bz2
B3X11_01_0049.cbf.bz2
B3X11_01_0050.cbf.bz2
B3X11_01_0051.cbf.bz2
B3X11_01_0052.cbf.bz2
B3X11_01_0053.cbf.bz2
B3X11_01_0054.cbf.bz2
B3X11_01_0055.cbf.bz2
B3X11_01_0056.cbf.bz2
B3X11_01_0057.cbf.bz2
B3X11_01_0058.cbf.bz2
B3X11_01_0059.cbf.bz2
B3X11_01_0060.cbf.bz2
B3X11_01_0061.cbf.bz2
B3X11_01_0062.cbf.bz2
B3X11_01_0063.cbf.bz2
B3X11_01_0064.cbf.bz2
B3X11_01_0065.cbf.bz2
B3X11_01_0066.cbf.bz2
B3X11_01_0067.cbf.bz2
B3X11_01_0068.cbf.bz2
B3X11_01_0069.cbf.bz2
B3X11_01_0070.cbf.bz2
B3X11_01_0071.cbf.bz2
B3X11_01_0072.cbf.bz2
B3X11_01_0073.cbf.bz2
B3X11_01_0074.cbf.bz2
B3X11_01_0075.cbf.bz2
B3X11_01_0076.cbf.bz2
B3X11_01_0077.cbf.bz2
B3X11_01_0078.cbf.bz2
B3X11_01_0079.cbf.bz2
B3X11_01_0080.cbf.bz2
B3X11_01_0081.cbf.bz2
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B3X11_01_0086.cbf.bz2
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B3X11_01_0088.cbf.bz2
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B3X11_01_0194.cbf.bz2
B3X11_01_0195.cbf.bz2
B3X11_01_0196.cbf.bz2
B3X11_01_0197.cbf.bz2
B3X11_01_0198.cbf.bz2
B3X11_01_0199.cbf.bz2
B3X11_01_0200.cbf.bz2
B3X11_01_0201.cbf.bz2
B3X11_01_0202.cbf.bz2
B3X11_01_0203.cbf.bz2
B3X11_01_0204.cbf.bz2
B3X11_01_0205.cbf.bz2
B3X11_01_0206.cbf.bz2
B3X11_01_0207.cbf.bz2
B3X11_01_0208.cbf.bz2
B3X11_01_0209.cbf.bz2
B3X11_01_0210.cbf.bz2
B3X11_01_0211.cbf.bz2
B3X11_01_0212.cbf.bz2
B3X11_01_0213.cbf.bz2
B3X11_01_0214.cbf.bz2
B3X11_01_0215.cbf.bz2
B3X11_01_0216.cbf.bz2
B3X11_01_0217.cbf.bz2
B3X11_01_0218.cbf.bz2
B3X11_01_0219.cbf.bz2
B3X11_01_0220.cbf.bz2
B3X11_01_0221.cbf.bz2
B3X11_01_0222.cbf.bz2
B3X11_01_0223.cbf.bz2
B3X11_01_0224.cbf.bz2
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B3X11_01_0226.cbf.bz2
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B3X11_01_0232.cbf.bz2
B3X11_01_0233.cbf.bz2
B3X11_01_0234.cbf.bz2
B3X11_01_0235.cbf.bz2
B3X11_01_0236.cbf.bz2
B3X11_01_0237.cbf.bz2
B3X11_01_0238.cbf.bz2
B3X11_01_0239.cbf.bz2
B3X11_01_0240.cbf.bz2
B3X11_01_0241.cbf.bz2
B3X11_01_0242.cbf.bz2
B3X11_01_0243.cbf.bz2
B3X11_01_0244.cbf.bz2
B3X11_01_0245.cbf.bz2
B3X11_01_0246.cbf.bz2
B3X11_01_0247.cbf.bz2
B3X11_01_0248.cbf.bz2
B3X11_01_0249.cbf.bz2
B3X11_01_0250.cbf.bz2
B3X11_01_0251.cbf.bz2
B3X11_01_0252.cbf.bz2
B3X11_01_0253.cbf.bz2
B3X11_01_0254.cbf.bz2
B3X11_01_0255.cbf.bz2
B3X11_01_0256.cbf.bz2
B3X11_01_0257.cbf.bz2
B3X11_01_0258.cbf.bz2
B3X11_01_0259.cbf.bz2
B3X11_01_0260.cbf.bz2
B3X11_01_0261.cbf.bz2
B3X11_01_0262.cbf.bz2
B3X11_01_0263.cbf.bz2
B3X11_01_0264.cbf.bz2
B3X11_01_0265.cbf.bz2
B3X11_01_0266.cbf.bz2
B3X11_01_0267.cbf.bz2
B3X11_01_0268.cbf.bz2
B3X11_01_0269.cbf.bz2
B3X11_01_0270.cbf.bz2
...
B3X11_10_0001.cbf.bz2
B3X11_10_0002.cbf.bz2
B3X11_10_0003.cbf.bz2
B3X11_10_0004.cbf.bz2
B3X11_10_0005.cbf.bz2
B3X11_10_0006.cbf.bz2
B3X11_10_0007.cbf.bz2
B3X11_10_0008.cbf.bz2
B3X11_10_0009.cbf.bz2
B3X11_10_0010.cbf.bz2
B3X11_10_0011.cbf.bz2
B3X11_10_0012.cbf.bz2
B3X11_10_0013.cbf.bz2
B3X11_10_0014.cbf.bz2
B3X11_10_0015.cbf.bz2
B3X11_10_0016.cbf.bz2
B3X11_10_0017.cbf.bz2
B3X11_10_0018.cbf.bz2
B3X11_10_0019.cbf.bz2
B3X11_10_0020.cbf.bz2
B3X11_10_0021.cbf.bz2
B3X11_10_0022.cbf.bz2
B3X11_10_0023.cbf.bz2
B3X11_10_0024.cbf.bz2
B3X11_10_0025.cbf.bz2
B3X11_10_0026.cbf.bz2
B3X11_10_0027.cbf.bz2
B3X11_10_0028.cbf.bz2
B3X11_10_0029.cbf.bz2
B3X11_10_0030.cbf.bz2
B3X11_10_0031.cbf.bz2
B3X11_10_0032.cbf.bz2
B3X11_10_0033.cbf.bz2
B3X11_10_0034.cbf.bz2
B3X11_10_0035.cbf.bz2
B3X11_10_0036.cbf.bz2
B3X11_10_0037.cbf.bz2
B3X11_10_0038.cbf.bz2
B3X11_10_0039.cbf.bz2
B3X11_10_0040.cbf.bz2
B3X11_10_0041.cbf.bz2
B3X11_10_0042.cbf.bz2
B3X11_10_0043.cbf.bz2
B3X11_10_0044.cbf.bz2
B3X11_10_0045.cbf.bz2
B3X11_10_0046.cbf.bz2
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B3X11_10_0060.cbf.bz2
B3X11_10_0061.cbf.bz2
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B3X11_10_0064.cbf.bz2
B3X11_10_0065.cbf.bz2
B3X11_10_0066.cbf.bz2
B3X11_10_0067.cbf.bz2
B3X11_10_0068.cbf.bz2
B3X11_10_0069.cbf.bz2
B3X11_10_0070.cbf.bz2
B3X11_10_0071.cbf.bz2
B3X11_10_0072.cbf.bz2
B3X11_10_0073.cbf.bz2
B3X11_10_0074.cbf.bz2
B3X11_10_0075.cbf.bz2
B3X11_10_0076.cbf.bz2
B3X11_10_0077.cbf.bz2
B3X11_10_0078.cbf.bz2
B3X11_10_0079.cbf.bz2
B3X11_10_0080.cbf.bz2
B3X11_10_0081.cbf.bz2
B3X11_10_0082.cbf.bz2
B3X11_10_0083.cbf.bz2
B3X11_10_0084.cbf.bz2
B3X11_10_0085.cbf.bz2
B3X11_10_0086.cbf.bz2
B3X11_10_0087.cbf.bz2
B3X11_10_0088.cbf.bz2
B3X11_10_0089.cbf.bz2
B3X11_10_0090.cbf.bz2
B3X11_10_0181.cbf.bz2
B3X11_10_0182.cbf.bz2
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B3X11_10_0189.cbf.bz2
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B3X11_10_0191.cbf.bz2
B3X11_10_0192.cbf.bz2
B3X11_10_0193.cbf.bz2
B3X11_10_0194.cbf.bz2
B3X11_10_0195.cbf.bz2
B3X11_10_0196.cbf.bz2
B3X11_10_0197.cbf.bz2
B3X11_10_0198.cbf.bz2
B3X11_10_0199.cbf.bz2
B3X11_10_0200.cbf.bz2
B3X11_10_0201.cbf.bz2
B3X11_10_0202.cbf.bz2
B3X11_10_0203.cbf.bz2
B3X11_10_0204.cbf.bz2
B3X11_10_0205.cbf.bz2
B3X11_10_0206.cbf.bz2
B3X11_10_0207.cbf.bz2
B3X11_10_0208.cbf.bz2
B3X11_10_0209.cbf.bz2
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B3X11_10_0211.cbf.bz2
B3X11_10_0212.cbf.bz2
B3X11_10_0213.cbf.bz2
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B3X11_10_0215.cbf.bz2
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B3X11_10_0218.cbf.bz2
B3X11_10_0219.cbf.bz2
B3X11_10_0220.cbf.bz2
B3X11_10_0221.cbf.bz2
B3X11_10_0222.cbf.bz2
B3X11_10_0223.cbf.bz2
B3X11_10_0224.cbf.bz2
B3X11_10_0225.cbf.bz2
B3X11_10_0226.cbf.bz2
B3X11_10_0227.cbf.bz2
B3X11_10_0228.cbf.bz2
B3X11_10_0229.cbf.bz2
B3X11_10_0230.cbf.bz2
B3X11_10_0231.cbf.bz2
B3X11_10_0232.cbf.bz2
B3X11_10_0233.cbf.bz2
B3X11_10_0234.cbf.bz2
B3X11_10_0235.cbf.bz2
B3X11_10_0236.cbf.bz2
B3X11_10_0237.cbf.bz2
B3X11_10_0238.cbf.bz2
B3X11_10_0239.cbf.bz2
B3X11_10_0240.cbf.bz2
B3X11_10_0241.cbf.bz2
B3X11_10_0242.cbf.bz2
B3X11_10_0243.cbf.bz2
B3X11_10_0244.cbf.bz2
B3X11_10_0245.cbf.bz2
B3X11_10_0246.cbf.bz2
B3X11_10_0247.cbf.bz2
B3X11_10_0248.cbf.bz2
B3X11_10_0249.cbf.bz2
B3X11_10_0250.cbf.bz2
B3X11_10_0251.cbf.bz2
B3X11_10_0252.cbf.bz2
B3X11_10_0253.cbf.bz2
B3X11_10_0254.cbf.bz2
B3X11_10_0255.cbf.bz2
B3X11_10_0256.cbf.bz2
B3X11_10_0257.cbf.bz2
B3X11_10_0258.cbf.bz2
B3X11_10_0259.cbf.bz2
B3X11_10_0260.cbf.bz2
B3X11_10_0261.cbf.bz2
B3X11_10_0262.cbf.bz2
B3X11_10_0263.cbf.bz2
B3X11_10_0264.cbf.bz2
B3X11_10_0265.cbf.bz2
B3X11_10_0266.cbf.bz2
B3X11_10_0267.cbf.bz2
B3X11_10_0268.cbf.bz2
B3X11_10_0269.cbf.bz2
B3X11_10_0270.cbf.bz2
@mysecondnameisdanger
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Datasets in between were deleted from the ls -1 command because... the comment was too big according to github.

@dagewa
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dagewa commented Mar 17, 2024

Hi, I don't think this is because the data sets are too different to be merged (that might be true, but probably isn't the cause of this error). This might be difficult to debug, but as a start could you please share the files /home/msnid/DEFAULT/scale/282_refined_cell.expt and /home/msnid/DEFAULT/scale/281_scaled.refl using some file sharing service?

@mysecondnameisdanger
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https://u.pcloud.link/publink/show?code=XZcytF0ZinOGaXtI5g4Wvf6mQcNUv5Kh7t5V
https://u.pcloud.link/publink/show?code=XZk7tF0ZuXDAhG0laO5kN56mR6e4PBD4vr5k
Thanks
Let me know if you need anything else.

@dagewa
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dagewa commented Mar 18, 2024

Thanks, I can see the problem. For the developers, we have this

In [1]: batch_offsets
Out[1]: 
[0,
 180,
 0,
 180,
 0,
 180,
 0,
 180,
 0,
 180,
 0,
 180,
 0,
 180,
 0,
 180,
 0,
 180,
 0,
 180]

In [2]: unique_offsets
Out[2]: {0, 180}

raising the error here:

dials/src/dials/util/export_mtz.py

Lines 670 to 677 in ea4fc09

if len(unique_offsets) != len(batch_offsets):
raise ValueError(
"Duplicate batch offsets detected: %s"
% ", ".join(
str(item) for item, count in Counter(batch_offsets).items() if count > 1
)
)

I don't understand the logic here. New batches are calculated on this condition:

dials/src/dials/util/export_mtz.py

Line 659 in ea4fc09

if len(set(unique_offsets)) <= 1:

but why <= 1? I would have thought what we need here would be

    if len(unique_offsets) != len(batch_offsets):

like the second condition further down.

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@dagewa @mysecondnameisdanger