Hi,
I'd like to reprocess some data that were collected on an Eiger2 detector at
Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a 64-bit
Windows 10 machine. The data were processed successfully at Diamond with no
obvious pathologies, the high resolution limit was just a little generous. The
folder in question contains a Diamond specific file (.nsx extension), two image
files (.h5), a header (.cbf), a master (.h5) and meta file (.h5). I've tried
pointing Xia2 to the folder itself (which works when processing data collected
on PILATUS detectors) and each of the files contained therein (except the
Diamond specific file). Each time this results in the error " -ERROR- None:56
Error in wrapper xia2_dials 0.0:: External process exited with exit code != 0
Process: C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials
0.0:: Error in checking external process after completion exit status and code:
0 1". I've attached the error, debug etc files for a representative 'run' to
this email. Which files do I need to point xia2 towards to get it to run? Any
help would be appreciated.
All the best,
Irwin
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Environment configuration...
Python => C:\CCP4-7\7.1\libexec\python.exe
CCTBX => C:\CCP4-7\7.1\lib\py2\site-packages
CCP4 => C:\CCP4-7\7.1
CCP4_SCR => c:\users\mfbx2is2\appdata\local\temp\tmpl7kddh
Starting directory:
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Working directory:
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Free space: 36.58 GB
Host: E-UL-MP16WKT4
Contact: xia2.supp...@gmail.com
XIA2 0.6.467-geb301d90-dials-2.2
DIALS 2.2.5-g89235367c-release
CCP4 7.1.005
Command line: xia2.bat pipeline=dials
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2_dials.phil
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7
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QFileSystemWatcher: skipping native engine, using only polling engine
QFileSystemWatcher: skipping native engine, using only polling engine
QFileSystemWatcher: failed to add paths:
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2.txt
QFileSystemWatcher: skipping native engine, using only polling engine
QFileSystemWatcher: skipping native engine, using only polling engine
QFileSystemWatcher: skipping native engine, using only polling engine
QFileSystemWatcher: skipping native engine, using only polling engine
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runTask Script raw Input Arguments
['C:\\CCP4-7\\7.1\\share\\ccp4i2\\bin\\runTask.py',
'C:\\Users\\MFBX2IS2\\CCP4I2_PROJECTS\\CYP141_258_7-2_reproc\\CCP4_JOBS\\job_1\\input_params.xml']
runTask Script top_path(CCPI2dir) and __file__ variables
C:\CCP4-7\7.1\share\ccp4i2 C:\CCP4-7\7.1\share\ccp4i2\bin\runTask.py
what is going on ? loadConfig
ccp4i2 version 1.0.2
ccp4i2 source revision 5710
Running QApplication to support asyncronous sub-processes
None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file C:\Users\MFBX2IS2\CCP4I2\db\database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
CRunPlugin.run before setupComAndLog
Starting core.CCP4DataManager.CDataManager 0.00499987602234
Running process xia2.bat asyncronously using QProcess
PROCESSMANAGER running command:
C:\CCP4-7\7.1\bin\xia2.bat pipeline=dials
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2_dials.phil
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7
>
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\log.txt
startQProcess process says finished -1073740940 1
Process finished: 1 exit code: -1073740940 exit status: 1 time: 09:29:38
22/Dec/2020
CPluginScript.handleProcessFailed processId 1 exitStatus 1 exitCode -1073740940
self._runningProcessId 1
CCP4Utils.getProgramVersion m1 ('Command line: ', ' pipeline=dials
C:\\Users\\MFBX2IS2\\CCP4I2_PROJECTS\\CYP141_258_7-2_reproc\\CCP4_JOBS\\job_1\\xia2_dials.phil
C:\\Users\\MFBX2IS2\\Desktop\\Diamond\\220919\\Raw\\7_2\\pos7_2_trip76\\dls\\i03\\data\\2019\\mx17773-76\\Cyp141\\Cyp141-73-76-258-7')
Failed adding program version to parent job xia2.bat None
Not backing up after possible sub-job
quitThread <core.CCP4PluginScript.CRunPlugin object at 0x0000000004387678>
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Environment configuration...
Python => C:\CCP4-7\7.1\libexec\python.exe
CCTBX => C:\CCP4-7\7.1\lib\py2\site-packages
CCP4 => C:\CCP4-7\7.1
CCP4_SCR => c:\users\mfbx2is2\appdata\local\temp\tmpl7kddh
Starting directory:
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Working directory:
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Free space: 36.58 GB
Host: E-UL-MP16WKT4
Contact: xia2.supp...@gmail.com
XIA2 0.6.467-geb301d90-dials-2.2
DIALS 2.2.5-g89235367c-release
CCP4 7.1.005
Command line: xia2.bat pipeline=dials
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2_dials.phil
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7
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Process ID: 2052
Environment configuration...
Python => C:\CCP4-7\7.1\libexec\python.exe
CCTBX => C:\CCP4-7\7.1\lib\py2\site-packages
CCP4 => C:\CCP4-7\7.1
CCP4_SCR => c:\users\mfbx2is2\appdata\local\temp\tmpl7kddh
Starting directory:
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Working directory:
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1
Free space: 36.58 GB
Host: E-UL-MP16WKT4
Contact: xia2.supp...@gmail.com
XIA2 0.6.467-geb301d90-dials-2.2
DIALS 2.2.5-g89235367c-release
CCP4 7.1.005
Start parsing command line:
['C:\\CCP4-7\\7.1\\lib\\py2\\site-packages\\xia2\\command_line\\xia2_main.py',
'pipeline=dials',
'C:\\Users\\MFBX2IS2\\CCP4I2_PROJECTS\\CYP141_258_7-2_reproc\\CCP4_JOBS\\job_1\\xia2_dials.phil',
'C:\\Users\\MFBX2IS2\\Desktop\\Diamond\\220919\\Raw\\7_2\\pos7_2_trip76\\dls\\i03\\data\\2019\\mx17773-76\\Cyp141\\Cyp141-73-76-258-7']
DIALS pipeline selected
Project: AUTOMATIC
Crystal: DEFAULT
Difference PHIL:
dials {
outlier {
algorithm = Auto
}
scale {
model = Auto
}
}
xia2.settings {
input {
anomalous = false
xinfo =
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1/automatic.xinfo
}
resolution {
keep_all_reflections = false
d_min = 2.1
}
multi_sweep_indexing = False
indexer = xds xdsii *dials
refiner = xds *dials
integrater = xdsr xds *dials
scaler = ccp4a xdsa *dials
multiprocessing {
nproc = 1
njob = 1
}
}
Working PHIL:
general {
check_image_files_readable = True
}
xds {
hdf5_plugin = "durin-plugin.so"
z_min = 0.0
delphi = 5
delphi_small = 30
untrusted_ellipse = None
untrusted_rectangle = None
trusted_region = None
backstop_mask = None
profile_grid_size = None
keep_outliers = True
correct {
refine = *DISTANCE *BEAM *AXIS *ORIENTATION *CELL *POSITION
air = None
}
integrate {
refine = *ORIENTATION *CELL *BEAM *DISTANCE AXIS *POSITION
refine_final = *ORIENTATION *CELL BEAM *DISTANCE AXIS *POSITION
fix_scale = False
delphi = 0
reflecting_range = 0
reflecting_range_esd = 0
beam_divergence = 0
beam_divergence_esd = 0
reintegrate = true
}
init {
fix_scale = False
}
defpix {
value_range_for_trusted_detector_pixels = None
}
index {
refine = *ORIENTATION *CELL *BEAM *DISTANCE *AXIS *POSITION
debug = *OFF ON
xparm = None
xparm_ub = None
max_wedge_size = 5
max_wedge_size_degrees = None
}
colspot {
minimum_pixels_per_spot = 1
}
xscale {
min_isigma = 3.0
zero_dose = False
}
merge2cbf {
merge_n_images = 2
data_range = None
moving_average = False
}
}
dials {
fix_geometry = False
outlier {
algorithm = Auto
}
check_indexing_symmetry = False
fast_mode = False
close_to_spindle_cutoff = 0.02
detect_blanks {
phi_step = 2.0
counts_fractional_loss = 0.1
misigma_fractional_loss = 0.1
}
masking {
border = 0
use_trusted_range = False
d_min = None
d_max = None
resolution_range = None
untrusted {
panel = 0
circle = None
rectangle = None
polygon = None
pixel = None
}
ice_rings {
filter = False
unit_cell = 4.498,4.498,7.338,90,90,120
space_group = 194
width = 0.002
d_min = None
}
}
find_spots {
phil_file = None
threshold.algorithm = dispersion dispersion_extended
min_spot_size = Auto
min_local = 0
sigma_strong = None
filter_ice_rings = False
kernel_size = 3
global_threshold = None
}
index {
phil_file = None
method = fft1d *fft3d real_space_grid_search
max_cell = 0.0
max_cell_estimation {
max_height_fraction = None
}
fft3d.n_points = None
reflections_per_degree = 100
histogram_binning = linear log
nearest_neighbor_percentile = None
}
refine {
phil_file = None
scan_static = True
scan_varying = True
interval_width_degrees = 36.0
reflections_per_degree = 100
}
integrate {
phil_file = None
background_outlier_algorithm = *null nsigma truncated normal plane tukey
background_algorithm = simple null *glm
combine_partials = True
partiality_threshold = 0.99
mosaic = *old new
scan_varying_profile = False
d_min = None
d_max = None
}
scale {
model = Auto
rotation_spacing = None
Bfactor = True
absorption = True
physical_model {
Bfactor_spacing = None
lmax = 4
}
array_model {
resolution_bins = 10
absorption_bins = 5
}
intensity_choice = profile summation *combine
error_model = *basic None
full_matrix = True
outlier_rejection = *standard simple
outlier_zmax = 6.0
partiality_threshold = 0.4
}
}
ccp4 {
reindex {
program = *pointless reindex cctbx
}
aimless {
intensities = summation profile *combine
surface_tie = 0.001
surface_link = True
rotation.spacing = 5
brotation.spacing = None
secondary {
frame = camera *crystal
lmax = 6
}
}
truncate {
program = ctruncate *cctbx
}
}
strategy {
name = None
description = None
i_over_sigi = 2.0
minimize_total_time = False
target_resolution = None
max_total_exposure = None
anomalous = False
dose_rate = 0.0
shape = 1.0
susceptibility = 1.0
completeness = 0.99
multiplicity = None
phi_range = None
min_oscillation_width = 0.05
xml_out = None
max_rotation_speed = None
min_exposure = None
}
xia2.settings {
pipeline = 3d 3dd 3di 3dii *dials dials-full dials-aimless
small_molecule = False
small_molecule_bfactor = True
failover = False
multi_crystal = False
interactive = False
project = AUTOMATIC
crystal = DEFAULT
input {
atom = None
anomalous = false
working_directory = None
image = None
json = None
reference_geometry = None
xinfo =
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1/automatic.xinfo
reverse_phi = False
gain = None
min_images = 10
min_oscillation_range = None
tolerance {
beam {
wavelength = 1e-06
direction = 1e-06
polarization_normal = 1e-06
polarization_fraction = 1e-06
}
detector {
fast_axis = 1e-06
slow_axis = 1e-06
origin = 0.05
}
goniometer {
rotation_axis = 1e-06
fixed_rotation = 1e-06
setting_rotation = 1e-06
}
scan {
oscillation = 0.01
}
}
geometry {
beam {
wavelength = None
direction = None
polarization_normal = None
polarization_fraction = None
}
detector {
panel {
id = 0
name = None
type = None
gain = None
pedestal = None
pixel_size = None
image_size = None
trusted_range = None
thickness = None
material = None
fast_axis = None
slow_axis = None
origin = None
parallax_correction = None
}
hierarchy {
name = None
fast_axis = None
slow_axis = None
origin = None
group {
id = None
name = None
fast_axis = None
slow_axis = None
origin = None
panel = None
}
}
mosflm_beam_centre = None
distance = None
slow_fast_beam_centre = None
}
goniometer {
axis = None
axes = None
angles = None
names = None
scan_axis = None
fixed_rotation = None
setting_rotation = None
invert_rotation_axis = False
}
scan {
image_range = None
extrapolate_scan = False
oscillation = None
batch_offset = None
}
convert_stills_to_sequences = False
convert_sequences_to_stills = False
}
format {
dynamic_shadowing = Auto
multi_panel = False
}
}
sweep {
id = None
range = None
exclude = False
}
scale {
directory = Auto
free_fraction = 0.05
free_total = None
freer_file = None
reference_reflection_file = None
reference_experiment_file = None
model = *decay *modulation *absorption partiality
scales = *rotation batch
two_theta_refine = True
}
space_group = None
unit_cell = None
resolution {
keep_all_reflections = false
d_max = None
d_min = 2.1
rmerge = None
completeness = None
cc_ref = 0.1
cc_half = 0.3
cc_half_method = *half_dataset sigma_tau
cc_half_significance_level = 0.1
cc_half_fit = polynomial *tanh
isigma = None
misigma = None
i_mean_over_sigma_mean = None
nbins = 100
reflections_per_bin = 10
binning_method = *counting_sorted volume
anomalous = False
labels = None
space_group = None
reference = None
}
unify_setting = False
trust_beam_centre = False
wavelength_tolerance = 5e-05
read_all_image_headers = True
detector_distance = None
show_template = False
untrusted_rectangle_indexing = None
xds_cell_deviation = 0.05, 5.0
xds_check_cell_deviation = False
use_brehm_diederichs = False
integration {
profile_fitting = True
exclude_ice_regions = False
}
developmental {
continue_from_previous_job = False
use_dials_spotfinder = False
pointless_tolerance = 0.0
detector_id = None
}
multi_sweep_indexing = False
remove_blanks = False
integrate_p1 = False
reintegrate_correct_lattice = True
lattice_rejection = True
lattice_rejection_threshold = 1.5
xds {
geometry_x = None
geometry_y = None
}
indexer = xds xdsii *dials
refiner = xds *dials
integrater = xdsr xds *dials
scaler = ccp4a xdsa *dials
merging_statistics {
source = aimless *cctbx
n_bins = 20
use_internal_variance = False
eliminate_sys_absent = False
}
verbose = False
multiprocessing {
mode = *serial parallel
nproc = 1
njob = 1
type = *simple qsub
qsub_command = ''
}
report {
d_min = None
d_max = None
resolution_bins = 20
anomalous = False
use_internal_variance = False
eliminate_sys_absent = False
range {
width = 1.0
min = None
max = None
}
cc_half_significance_level = 0.01
cc_half_method = *half_dataset sigma_tau
chef_min_completeness = None
dose {
remove_gaps = True
batch {
range = None
dose_start = None
dose_step = None
}
}
xtriage_analysis = True
include_radiation_damage = True
batch {
id = None
range = None
}
}
symmetry {
chirality = chiral nonchiral centrosymmetric
program = *pointless dials
}
}
Command line: xia2.bat pipeline=dials
C:\Users\MFBX2IS2\CCP4I2_PROJECTS\CYP141_258_7-2_reproc\CCP4_JOBS\job_1\xia2_dials.phil
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7
Exception A: template not recognised for Cyp141-73-76-258-7_2_header.cbf
(C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_header.cbf)
Traceback (most recent call last):
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Applications\xia2setup.py",
line 158, in get_template
template, directory = image2template_directory(f)
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Experts\FindImages.py", line
99, in image2template_directory
template = image2template(image)
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Experts\FindImages.py", line
82, in image2template
return template_regex(filename)[0]
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Experts\FindImages.py", line
61, in template_regex
raise RuntimeError("template not recognised for %s" % filename)
RuntimeError: template not recognised for Cyp141-73-76-258-7_2_header.cbf
Exception B: template not recognised for
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_header.cbf
Traceback (most recent call last):
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Applications\xia2setup.py",
line 209, in visit
template = get_template(full_path)
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Applications\xia2setup.py",
line 170, in get_template
raise RuntimeError("template not recognised for %s" % f)
RuntimeError: template not recognised for
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_header.cbf
Using FormatRawData for
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_000002.h5
Loaded file:
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_000002.h5
Added imageset to datablock 0
Exception C: no imageset found
(C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_000002.h5)
Traceback (most recent call last):
File
"C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Applications\xia2setup_helpers.py",
line 17, in get_sweep
sweeplist = SweepFactory(template, directory)
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Schema\Sweep.py", line 21, in
SweepFactory
template, directory,
reversephi=PhilIndex.params.xia2.settings.input.reverse_phi
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Schema\__init__.py", line 160,
in load_imagesets
assert len(imagesets) > 0, "no imageset found"
AssertionError: no imageset found
Using FormatHDF5 for
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_meta.h5
Exception C:
(C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_meta.h5)
Traceback (most recent call last):
File
"C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Applications\xia2setup_helpers.py",
line 17, in get_sweep
sweeplist = SweepFactory(template, directory)
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Schema\Sweep.py", line 21, in
SweepFactory
template, directory,
reversephi=PhilIndex.params.xia2.settings.input.reverse_phi
File "C:\CCP4-7\7.1\lib\py2\site-packages\xia2\Schema\__init__.py", line 116,
in load_imagesets
format_kwargs=format_kwargs,
File "C:\CCP4-7\7.1\lib\py2\site-packages\dxtbx\model\experiment_list.py",
line 537, in from_filenames
format_kwargs=format_kwargs,
File "C:\CCP4-7\7.1\lib\py2\site-packages\dxtbx\datablock.py", line 1529, in
from_filenames
format_kwargs=format_kwargs,
File "C:\CCP4-7\7.1\lib\py2\site-packages\dxtbx\datablock.py", line 965, in
__init__
format_class, filename, format_kwargs=format_kwargs
File "C:\CCP4-7\7.1\lib\py2\site-packages\dxtbx\datablock.py", line 1185, in
_create_single_file_imageset
return format_class.get_imageset(abspath(filename),
format_kwargs=format_kwargs)
File "C:\CCP4-7\7.1\lib\py2\site-packages\dxtbx\format\FormatMultiImage.py",
line 135, in get_imageset
assert single_file_indices is not None
AssertionError
Using FormatNexusEigerDLS16M for
C:\Users\MFBX2IS2\Desktop\Diamond\220919\Raw\7_2\pos7_2_trip76\dls\i03\data\2019\mx17773-76\Cyp141\Cyp141-73-76-258-7\Cyp141-73-76-258-7_2_master.h5
########################################################################
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