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Andrea Nans
Feb 26, 2016, 6:07:50 AM2/26/16
to emspring
Hello,
(Using most up to date version of spring)
I'm having a strange error when trying to run segmentexam on my own data of segments. For some reason, it thinks the segments were binned by 0 and then exits with the error:
INFO:CPU0:bin_image_stack_by_binfactor:The following segments were binned by a factor 0 for further analysis and saved in /tmp/andrean-26_Feb_2016_10_48_51-14722
/seg4class.hdf.
File "/home/andrean/spring_v0-84-1470/bin/segmentexam_mpi", line 152, in <module>
sys.exit(spring.segment2d.segmentexam_mpi.main())
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 175, in main
stack.add_up_power_spectra()
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 153, in add_up_power_
spectra
segment_ids = self.prepare_segmentexam_mpi()
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 52, in prepare_segmen
texam_mpi
self.infilestack, self.segsizepix, self.helixwidthpix, self.pixelsize, segment_ids, binned_stack)
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam.py", line 200, in apply_binfactor
helixwidthpix = helixwidthpix/binfactor
ZeroDivisionError: integer division or modulo by zero
Any idea why it's using bin factor of 0 instead of 1? The TMV tutorial did not give me this error--
Many thanks,
Andrea
Francis Crick Institute
(Using most up to date version of spring)
I'm having a strange error when trying to run segmentexam on my own data of segments. For some reason, it thinks the segments were binned by 0 and then exits with the error:
INFO:CPU0:bin_image_stack_by_binfactor:The following segments were binned by a factor 0 for further analysis and saved in /tmp/andrean-26_Feb_2016_10_48_51-14722
/seg4class.hdf.
File "/home/andrean/spring_v0-84-1470/bin/segmentexam_mpi", line 152, in <module>
sys.exit(spring.segment2d.segmentexam_mpi.main())
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 175, in main
stack.add_up_power_spectra()
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 153, in add_up_power_
spectra
segment_ids = self.prepare_segmentexam_mpi()
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py", line 52, in prepare_segmen
texam_mpi
self.infilestack, self.segsizepix, self.helixwidthpix, self.pixelsize, segment_ids, binned_stack)
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam.py", line 200, in apply_binfactor
helixwidthpix = helixwidthpix/binfactor
ZeroDivisionError: integer division or modulo by zero
Any idea why it's using bin factor of 0 instead of 1? The TMV tutorial did not give me this error--
Many thanks,
Andrea
Francis Crick Institute
Carsten Sachse
Feb 26, 2016, 5:08:00 PM2/26/16
to emsp...@googlegroups.com
Dear Andrea,
Could you provide your input parameters for diagnosis of the issue?
Thanks.
Best wishes,
Carsten
Andrea Nans
Mar 1, 2016, 6:47:18 AM3/1/16
to emspring
Hello,
I am pasting the log so that you can see the input parameters and the full output from the process.
Thanks,
Andrea
INFO:CPU0:startlog:
INFO:CPU0:startlog:The following input parameters have been received:
INFO:CPU0:startlog:Image input stack = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/flu_4class.hdf
INFO:CPU0:startlog:Diagnostic plot = diag.pdf
INFO:CPU0:startlog:Power spectrum output image = power.hdf
INFO:CPU0:startlog:Enhanced power spectrum option = None
INFO:CPU0:startlog:Enhanced power spectrum output image = None
INFO:CPU0:startlog:Pixel size in Angstrom = 7.0
INFO:CPU0:startlog:Estimated helix width in Angstrom = 230
INFO:CPU0:startlog:Power spectrum resolution cutoff in 1/Angstrom = None
INFO:CPU0:startlog:Compute layer-line correlation option = None
INFO:CPU0:startlog:Layer-line region in 1/Angstrom = None
INFO:CPU0:startlog:Reference power spectrum = None
INFO:CPU0:startlog:Power spectrum input image = None
INFO:CPU0:startlog:spring.db file = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/spring.db
INFO:CPU0:startlog:Micrographs select option = None
INFO:CPU0:startlog:Include or exclude micrographs = None
INFO:CPU0:startlog:Micrographs list = None
INFO:CPU0:startlog:Helices select option = None
INFO:CPU0:startlog:Include or exclude helices = None
INFO:CPU0:startlog:Helices list = None
INFO:CPU0:startlog:Segments select option = None
INFO:CPU0:startlog:Include or exclude segments = None
INFO:CPU0:startlog:Segment file = None
INFO:CPU0:startlog:Classes select option = None
INFO:CPU0:startlog:Include or exclude classes = None
INFO:CPU0:startlog:Class type = None
INFO:CPU0:startlog:Classes list = None
INFO:CPU0:startlog:Persistence class option = None
INFO:CPU0:startlog:Persistence class length in Angstrom = None
INFO:CPU0:startlog:Class occupancy threshold = None
INFO:CPU0:startlog:Straightness select option = None
INFO:CPU0:startlog:Include or exclude straight helices = None
INFO:CPU0:startlog:Persistence length range = None
INFO:CPU0:startlog:Layer line correlation select option = None
INFO:CPU0:startlog:Include or exclude segments based on layer-line correlation = None
INFO:CPU0:startlog:Correlation layer line range = None
INFO:CPU0:startlog:Defocus select option = None
INFO:CPU0:startlog:Include or exclude defocus range = None
INFO:CPU0:startlog:Defocus range = None
INFO:CPU0:startlog:Astigmatism select option = None
INFO:CPU0:startlog:Include or exclude astigmatic segments = None
INFO:CPU0:startlog:Astigmatism range = None
INFO:CPU0:startlog:MPI option = None
INFO:CPU0:startlog:Number of CPUs = None
INFO:CPU0:startlog:Temporary directory = None
INFO:CPU0:startlog:
----------------------------------------------------------------------------------------------------
The final set of parameters has been completed with the provided default parameters:
INFO:CPU0:startlog:Image input stack = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/flu_4class.hdf
INFO:CPU0:startlog:Diagnostic plot = diag.pdf
INFO:CPU0:startlog:Power spectrum output image = power.hdf
INFO:CPU0:startlog:Enhanced power spectrum option = True
INFO:CPU0:startlog:Enhanced power spectrum output image = power_enhanced.hdf
INFO:CPU0:startlog:Pixel size in Angstrom = 7.0
INFO:CPU0:startlog:Estimated helix width in Angstrom = 230
INFO:CPU0:startlog:Power spectrum resolution cutoff in 1/Angstrom = 0.15
INFO:CPU0:startlog:Compute layer-line correlation option = False
INFO:CPU0:startlog:Layer-line region in 1/Angstrom = (0.03, 0.035)
INFO:CPU0:startlog:Reference power spectrum = False
INFO:CPU0:startlog:Power spectrum input image = power.hdf
INFO:CPU0:startlog:spring.db file = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/spring.db
INFO:CPU0:startlog:Micrographs select option = False
INFO:CPU0:startlog:Include or exclude micrographs = include
INFO:CPU0:startlog:Micrographs list = 1-9, 11, 13
INFO:CPU0:startlog:Helices select option = False
INFO:CPU0:startlog:Include or exclude helices = include
INFO:CPU0:startlog:Helices list = 1-9, 11, 13
INFO:CPU0:startlog:Segments select option = False
INFO:CPU0:startlog:Include or exclude segments = include
INFO:CPU0:startlog:Segment file = stackid_file.dat
INFO:CPU0:startlog:Classes select option = False
INFO:CPU0:startlog:Include or exclude classes = include
INFO:CPU0:startlog:Class type = class_id
INFO:CPU0:startlog:Classes list = 1-9, 11, 13
INFO:CPU0:startlog:Persistence class option = False
INFO:CPU0:startlog:Persistence class length in Angstrom = 700
INFO:CPU0:startlog:Class occupancy threshold = 0.5
INFO:CPU0:startlog:Straightness select option = False
INFO:CPU0:startlog:Include or exclude straight helices = include
INFO:CPU0:startlog:Persistence length range = (80, 100)
INFO:CPU0:startlog:Layer line correlation select option = False
INFO:CPU0:startlog:Include or exclude segments based on layer-line correlation = include
INFO:CPU0:startlog:Correlation layer line range = (60, 100)
INFO:CPU0:startlog:Defocus select option = False
INFO:CPU0:startlog:Include or exclude defocus range = include
INFO:CPU0:startlog:Defocus range = (10000, 40000)
INFO:CPU0:startlog:Astigmatism select option = False
INFO:CPU0:startlog:Include or exclude astigmatic segments = include
INFO:CPU0:startlog:Astigmatism range = (0, 4000)
INFO:CPU0:startlog:MPI option = True
INFO:CPU0:startlog:Number of CPUs = 6
INFO:CPU0:startlog:Temporary directory = /tmp
INFO:CPU0:startlog:
############################################ START ############################################
INFO:CPU0:startlog:progress state: 1 % [> ]
INFO:andrean:/home/andrean/spring_v0-84-1470/parts/openmpi/bin/mpirun -np 6 /home/andrean/spring_v0-84-1470/bin/segmentexam_mpi --f par
file_2841.par --d . --l report.log
logged on Thu, 25 Feb 2016 17:16:24
INFO:andrean:
####################################################################################################
Beginning of the program segmentexam (Emspring v0.84.1470): Thu, 25 Feb 2016 17:16:30
####################################################################################################
INFO:andrean:
############################################ INPUT ############################################
INFO:CPU0:startlog:
INFO:CPU0:startlog:The following input parameters have been received:
INFO:CPU0:startlog:Image input stack = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/flu_4class.hdf
INFO:CPU0:startlog:Diagnostic plot = diag.pdf
INFO:CPU0:startlog:Power spectrum output image = power.hdf
INFO:CPU0:startlog:Enhanced power spectrum option = True
INFO:CPU0:startlog:Enhanced power spectrum output image = power_enhanced.hdf
INFO:CPU0:startlog:Pixel size in Angstrom = 7.0
INFO:CPU0:startlog:Estimated helix width in Angstrom = 230
INFO:CPU0:startlog:Power spectrum resolution cutoff in 1/Angstrom = 0.15
INFO:CPU0:startlog:Compute layer-line correlation option = False
INFO:CPU0:startlog:Layer-line region in 1/Angstrom = (0.03, 0.035)
INFO:CPU0:startlog:Reference power spectrum = False
INFO:CPU0:startlog:Power spectrum input image = power.hdf
INFO:CPU0:startlog:spring.db file = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/spring.db
INFO:CPU0:startlog:Micrographs select option = False
INFO:CPU0:startlog:Include or exclude micrographs = include
INFO:CPU0:startlog:Micrographs list = 1-9, 11, 13
INFO:CPU0:startlog:Helices select option = False
INFO:CPU0:startlog:Include or exclude helices = include
INFO:CPU0:startlog:Helices list = 1-9, 11, 13
INFO:CPU0:startlog:Segments select option = False
INFO:CPU0:startlog:Include or exclude segments = include
INFO:CPU0:startlog:Segment file = stackid_file.dat
INFO:CPU0:startlog:Classes select option = False
INFO:CPU0:startlog:Include or exclude classes = include
INFO:CPU0:startlog:Class type = class_id
INFO:CPU0:startlog:Classes list = 1-9, 11, 13
INFO:CPU0:startlog:Persistence class option = False
INFO:CPU0:startlog:Persistence class length in Angstrom = 700
INFO:CPU0:startlog:Class occupancy threshold = 0.5
INFO:CPU0:startlog:Straightness select option = False
INFO:CPU0:startlog:Include or exclude straight helices = include
INFO:CPU0:startlog:Persistence length range = (80, 100)
INFO:CPU0:startlog:Layer line correlation select option = False
INFO:CPU0:startlog:Include or exclude segments based on layer-line correlation = include
INFO:CPU0:startlog:Correlation layer line range = (60, 100)
INFO:CPU0:startlog:Defocus select option = False
INFO:CPU0:startlog:Include or exclude defocus range = include
INFO:CPU0:startlog:Defocus range = (10000, 40000)
INFO:CPU0:startlog:Astigmatism select option = False
INFO:CPU0:startlog:Include or exclude astigmatic segments = include
INFO:CPU0:startlog:Astigmatism range = (0, 4000)
INFO:CPU0:startlog:MPI option = True
INFO:CPU0:startlog:Number of CPUs = 6
INFO:CPU0:startlog:Temporary directory = /tmp
INFO:CPU0:startlog:
############################################ START ############################################
INFO:CPU0:startlog:progress state: 1 % [> ]
INFO:andrean:The following temporary directories were made:
rank_id node_name process_id directory space_required
--------- ------------------- ------------ --------------------------------------- ----------------
0 cryo2.ps.local.nimr 2847 /tmp/andrean-25_Feb_2016_17_16_30-2847/ 1.00GB
1 cryo2.ps.local.nimr 2855 /tmp/andrean-25_Feb_2016_17_16_30-2855/ 1000.01MB
2 cryo2.ps.local.nimr 2856 /tmp/andrean-25_Feb_2016_17_16_30-2856/ 1000.01MB
3 cryo2.ps.local.nimr 2880 /tmp/andrean-25_Feb_2016_17_16_30-2880/ 1000.01MB
4 cryo2.ps.local.nimr 2881 /tmp/andrean-25_Feb_2016_17_16_31-2881/ 1000.01MB
5 cryo2.ps.local.nimr 2891 /tmp/andrean-25_Feb_2016_17_16_31-2891/ 1000.01MB
INFO:andrean:The selection resulted in the following number of included and excluded segments:
total 1276
-------- ------
included 1276
excluded 0
The number of segments that were excluded listed by criteria:
--------------- -
seg_count 0
mic_count 0
helix_count 0
class_count 0
curvature_count 0
defocus_count 0
astig_count 0
layer_cc_count 0
--------------- -
The following 1276 segments are included in the selection:
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 3
6, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102,
103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156,
157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183,
184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210,
211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237,
238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264,
265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318,
319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345,
346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372,
373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399,
400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426,
427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453,
454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480,
481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507,
508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534,
535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561,
562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588,
589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615,
616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642,
643, 644, 645, 646, 647, 648, 649, 650, 651, 652, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669,
670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696,
697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723,
724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750,
751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777,
778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804,
805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 830, 831,
832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 845, 846, 847, 848, 849, 850, 851, 852, 853, 854, 855, 856, 857, 858,
859, 860, 861, 862, 863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882, 883, 884, 885,
886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911, 912,
913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939,
940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 965, 966,
967, 968, 969, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993,
994, 995, 996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 101
7, 1018, 1019, 1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031, 1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039,
1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 1060, 1061, 106
2, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084,
1085, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1105, 1106, 110
7, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127, 1128, 1129,
1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1150, 1151, 115
2, 1153, 1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1165, 1166, 1167, 1168, 1169, 1170, 1171, 1172, 1173, 1174,
1175, 1176, 1177, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1195, 1196, 119
7, 1198, 1199, 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1212, 1213, 1214, 1215, 1216, 1217, 1218, 1219,
1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1229, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 1240, 1241, 124
2, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264,
1265, 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275
INFO:CPU0:bin_image_stack_by_binfactor:
INFO:CPU4:bin_image_stack_by_binfactor:
INFO:CPU1:bin_image_stack_by_binfactor:
INFO:CPU2:bin_image_stack_by_binfactor:
INFO:CPU3:bin_image_stack_by_binfactor:
INFO:CPU5:bin_image_stack_by_binfactor:
I am pasting the log so that you can see the input parameters and the full output from the process.
Thanks,
Andrea
INFO:CPU0:startlog:
INFO:CPU0:startlog:The following input parameters have been received:
INFO:CPU0:startlog:Image input stack = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/flu_4class.hdf
INFO:CPU0:startlog:Diagnostic plot = diag.pdf
INFO:CPU0:startlog:Power spectrum output image = power.hdf
INFO:CPU0:startlog:Enhanced power spectrum option = None
INFO:CPU0:startlog:Enhanced power spectrum output image = None
INFO:CPU0:startlog:Pixel size in Angstrom = 7.0
INFO:CPU0:startlog:Estimated helix width in Angstrom = 230
INFO:CPU0:startlog:Power spectrum resolution cutoff in 1/Angstrom = None
INFO:CPU0:startlog:Compute layer-line correlation option = None
INFO:CPU0:startlog:Layer-line region in 1/Angstrom = None
INFO:CPU0:startlog:Reference power spectrum = None
INFO:CPU0:startlog:Power spectrum input image = None
INFO:CPU0:startlog:spring.db file = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/spring.db
INFO:CPU0:startlog:Micrographs select option = None
INFO:CPU0:startlog:Include or exclude micrographs = None
INFO:CPU0:startlog:Micrographs list = None
INFO:CPU0:startlog:Helices select option = None
INFO:CPU0:startlog:Include or exclude helices = None
INFO:CPU0:startlog:Helices list = None
INFO:CPU0:startlog:Segments select option = None
INFO:CPU0:startlog:Include or exclude segments = None
INFO:CPU0:startlog:Segment file = None
INFO:CPU0:startlog:Classes select option = None
INFO:CPU0:startlog:Include or exclude classes = None
INFO:CPU0:startlog:Class type = None
INFO:CPU0:startlog:Classes list = None
INFO:CPU0:startlog:Persistence class option = None
INFO:CPU0:startlog:Persistence class length in Angstrom = None
INFO:CPU0:startlog:Class occupancy threshold = None
INFO:CPU0:startlog:Straightness select option = None
INFO:CPU0:startlog:Include or exclude straight helices = None
INFO:CPU0:startlog:Persistence length range = None
INFO:CPU0:startlog:Layer line correlation select option = None
INFO:CPU0:startlog:Include or exclude segments based on layer-line correlation = None
INFO:CPU0:startlog:Correlation layer line range = None
INFO:CPU0:startlog:Defocus select option = None
INFO:CPU0:startlog:Include or exclude defocus range = None
INFO:CPU0:startlog:Defocus range = None
INFO:CPU0:startlog:Astigmatism select option = None
INFO:CPU0:startlog:Include or exclude astigmatic segments = None
INFO:CPU0:startlog:Astigmatism range = None
INFO:CPU0:startlog:MPI option = None
INFO:CPU0:startlog:Number of CPUs = None
INFO:CPU0:startlog:Temporary directory = None
INFO:CPU0:startlog:
----------------------------------------------------------------------------------------------------
The final set of parameters has been completed with the provided default parameters:
INFO:CPU0:startlog:Image input stack = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/flu_4class.hdf
INFO:CPU0:startlog:Diagnostic plot = diag.pdf
INFO:CPU0:startlog:Power spectrum output image = power.hdf
INFO:CPU0:startlog:Enhanced power spectrum option = True
INFO:CPU0:startlog:Enhanced power spectrum output image = power_enhanced.hdf
INFO:CPU0:startlog:Pixel size in Angstrom = 7.0
INFO:CPU0:startlog:Estimated helix width in Angstrom = 230
INFO:CPU0:startlog:Power spectrum resolution cutoff in 1/Angstrom = 0.15
INFO:CPU0:startlog:Compute layer-line correlation option = False
INFO:CPU0:startlog:Layer-line region in 1/Angstrom = (0.03, 0.035)
INFO:CPU0:startlog:Reference power spectrum = False
INFO:CPU0:startlog:Power spectrum input image = power.hdf
INFO:CPU0:startlog:spring.db file = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/spring.db
INFO:CPU0:startlog:Micrographs select option = False
INFO:CPU0:startlog:Include or exclude micrographs = include
INFO:CPU0:startlog:Micrographs list = 1-9, 11, 13
INFO:CPU0:startlog:Helices select option = False
INFO:CPU0:startlog:Include or exclude helices = include
INFO:CPU0:startlog:Helices list = 1-9, 11, 13
INFO:CPU0:startlog:Segments select option = False
INFO:CPU0:startlog:Include or exclude segments = include
INFO:CPU0:startlog:Segment file = stackid_file.dat
INFO:CPU0:startlog:Classes select option = False
INFO:CPU0:startlog:Include or exclude classes = include
INFO:CPU0:startlog:Class type = class_id
INFO:CPU0:startlog:Classes list = 1-9, 11, 13
INFO:CPU0:startlog:Persistence class option = False
INFO:CPU0:startlog:Persistence class length in Angstrom = 700
INFO:CPU0:startlog:Class occupancy threshold = 0.5
INFO:CPU0:startlog:Straightness select option = False
INFO:CPU0:startlog:Include or exclude straight helices = include
INFO:CPU0:startlog:Persistence length range = (80, 100)
INFO:CPU0:startlog:Layer line correlation select option = False
INFO:CPU0:startlog:Include or exclude segments based on layer-line correlation = include
INFO:CPU0:startlog:Correlation layer line range = (60, 100)
INFO:CPU0:startlog:Defocus select option = False
INFO:CPU0:startlog:Include or exclude defocus range = include
INFO:CPU0:startlog:Defocus range = (10000, 40000)
INFO:CPU0:startlog:Astigmatism select option = False
INFO:CPU0:startlog:Include or exclude astigmatic segments = include
INFO:CPU0:startlog:Astigmatism range = (0, 4000)
INFO:CPU0:startlog:MPI option = True
INFO:CPU0:startlog:Number of CPUs = 6
INFO:CPU0:startlog:Temporary directory = /tmp
INFO:CPU0:startlog:
############################################ START ############################################
INFO:CPU0:startlog:progress state: 1 % [> ]
INFO:andrean:/home/andrean/spring_v0-84-1470/parts/openmpi/bin/mpirun -np 6 /home/andrean/spring_v0-84-1470/bin/segmentexam_mpi --f par
file_2841.par --d . --l report.log
logged on Thu, 25 Feb 2016 17:16:24
INFO:andrean:
####################################################################################################
Beginning of the program segmentexam (Emspring v0.84.1470): Thu, 25 Feb 2016 17:16:30
####################################################################################################
INFO:andrean:
############################################ INPUT ############################################
INFO:CPU0:startlog:
INFO:CPU0:startlog:The following input parameters have been received:
INFO:CPU0:startlog:Image input stack = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/flu_4class.hdf
INFO:CPU0:startlog:Diagnostic plot = diag.pdf
INFO:CPU0:startlog:Power spectrum output image = power.hdf
INFO:CPU0:startlog:Enhanced power spectrum option = True
INFO:CPU0:startlog:Enhanced power spectrum output image = power_enhanced.hdf
INFO:CPU0:startlog:Pixel size in Angstrom = 7.0
INFO:CPU0:startlog:Estimated helix width in Angstrom = 230
INFO:CPU0:startlog:Power spectrum resolution cutoff in 1/Angstrom = 0.15
INFO:CPU0:startlog:Compute layer-line correlation option = False
INFO:CPU0:startlog:Layer-line region in 1/Angstrom = (0.03, 0.035)
INFO:CPU0:startlog:Reference power spectrum = False
INFO:CPU0:startlog:Power spectrum input image = power.hdf
INFO:CPU0:startlog:spring.db file = /home/andrean/FluC/segment_25_Feb_2016_17_15_07_2540/spring.db
INFO:CPU0:startlog:Micrographs select option = False
INFO:CPU0:startlog:Include or exclude micrographs = include
INFO:CPU0:startlog:Micrographs list = 1-9, 11, 13
INFO:CPU0:startlog:Helices select option = False
INFO:CPU0:startlog:Include or exclude helices = include
INFO:CPU0:startlog:Helices list = 1-9, 11, 13
INFO:CPU0:startlog:Segments select option = False
INFO:CPU0:startlog:Include or exclude segments = include
INFO:CPU0:startlog:Segment file = stackid_file.dat
INFO:CPU0:startlog:Classes select option = False
INFO:CPU0:startlog:Include or exclude classes = include
INFO:CPU0:startlog:Class type = class_id
INFO:CPU0:startlog:Classes list = 1-9, 11, 13
INFO:CPU0:startlog:Persistence class option = False
INFO:CPU0:startlog:Persistence class length in Angstrom = 700
INFO:CPU0:startlog:Class occupancy threshold = 0.5
INFO:CPU0:startlog:Straightness select option = False
INFO:CPU0:startlog:Include or exclude straight helices = include
INFO:CPU0:startlog:Persistence length range = (80, 100)
INFO:CPU0:startlog:Layer line correlation select option = False
INFO:CPU0:startlog:Include or exclude segments based on layer-line correlation = include
INFO:CPU0:startlog:Correlation layer line range = (60, 100)
INFO:CPU0:startlog:Defocus select option = False
INFO:CPU0:startlog:Include or exclude defocus range = include
INFO:CPU0:startlog:Defocus range = (10000, 40000)
INFO:CPU0:startlog:Astigmatism select option = False
INFO:CPU0:startlog:Include or exclude astigmatic segments = include
INFO:CPU0:startlog:Astigmatism range = (0, 4000)
INFO:CPU0:startlog:MPI option = True
INFO:CPU0:startlog:Number of CPUs = 6
INFO:CPU0:startlog:Temporary directory = /tmp
INFO:CPU0:startlog:
############################################ START ############################################
INFO:CPU0:startlog:progress state: 1 % [> ]
INFO:andrean:The following temporary directories were made:
rank_id node_name process_id directory space_required
--------- ------------------- ------------ --------------------------------------- ----------------
0 cryo2.ps.local.nimr 2847 /tmp/andrean-25_Feb_2016_17_16_30-2847/ 1.00GB
1 cryo2.ps.local.nimr 2855 /tmp/andrean-25_Feb_2016_17_16_30-2855/ 1000.01MB
2 cryo2.ps.local.nimr 2856 /tmp/andrean-25_Feb_2016_17_16_30-2856/ 1000.01MB
3 cryo2.ps.local.nimr 2880 /tmp/andrean-25_Feb_2016_17_16_30-2880/ 1000.01MB
4 cryo2.ps.local.nimr 2881 /tmp/andrean-25_Feb_2016_17_16_31-2881/ 1000.01MB
5 cryo2.ps.local.nimr 2891 /tmp/andrean-25_Feb_2016_17_16_31-2891/ 1000.01MB
INFO:andrean:The selection resulted in the following number of included and excluded segments:
total 1276
-------- ------
included 1276
excluded 0
The number of segments that were excluded listed by criteria:
--------------- -
seg_count 0
mic_count 0
helix_count 0
class_count 0
curvature_count 0
defocus_count 0
astig_count 0
layer_cc_count 0
--------------- -
The following 1276 segments are included in the selection:
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 3
6, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102,
103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156,
157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183,
184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210,
211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237,
238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264,
265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291,
292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318,
319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345,
346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372,
373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399,
400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426,
427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453,
454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480,
481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507,
508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534,
535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561,
562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588,
589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615,
616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642,
643, 644, 645, 646, 647, 648, 649, 650, 651, 652, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669,
670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696,
697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723,
724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750,
751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777,
778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804,
805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 830, 831,
832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 845, 846, 847, 848, 849, 850, 851, 852, 853, 854, 855, 856, 857, 858,
859, 860, 861, 862, 863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882, 883, 884, 885,
886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911, 912,
913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939,
940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 965, 966,
967, 968, 969, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993,
994, 995, 996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 101
7, 1018, 1019, 1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031, 1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039,
1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 1060, 1061, 106
2, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084,
1085, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1105, 1106, 110
7, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127, 1128, 1129,
1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1150, 1151, 115
2, 1153, 1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1165, 1166, 1167, 1168, 1169, 1170, 1171, 1172, 1173, 1174,
1175, 1176, 1177, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1195, 1196, 119
7, 1198, 1199, 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1212, 1213, 1214, 1215, 1216, 1217, 1218, 1219,
1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1229, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 1240, 1241, 124
2, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264,
1265, 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275
INFO:CPU0:bin_image_stack_by_binfactor:
INFO:CPU4:bin_image_stack_by_binfactor:
INFO:CPU1:bin_image_stack_by_binfactor:
INFO:CPU2:bin_image_stack_by_binfactor:
INFO:CPU3:bin_image_stack_by_binfactor:
INFO:CPU5:bin_image_stack_by_binfactor:
INFO:CPU0:bin_image_stack_by_binfactor:The following segments were binned by a factor 0 for further analysis and saved in /tmp/andrean-
25_Feb_2016_17_16_30-2847/flu_4class.hdf.
(Local_id, Segment_id)
(0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (1
7, 17) (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) (27, 27) (28, 28) (29, 29) (30, 30) (31, 31) (3
2, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, 38) (39, 39) (40, 40) (41, 41) (42, 42) (43, 43) (44, 44) (45, 45) (46, 46) (4
7, 47) (48, 48) (49, 49) (50, 50) (51, 51) (52, 52) (53, 53) (54, 54) (55, 55) (56, 56) (57, 57) (58, 58) (59, 59) (60, 60) (61, 61) (6
2, 62) (63, 63) (64, 64) (65, 65) (66, 66) (67, 67) (68, 68) (69, 69) (70, 70) (71, 71) (72, 72) (73, 73) (74, 74) (75, 75) (76, 76) (7
7, 77) (78, 78) (79, 79) (80, 80) (81, 81) (82, 82) (83, 83) (84, 84) (85, 85) (86, 86) (87, 87) (88, 88) (89, 89) (90, 90) (91, 91) (9
2, 92) (93, 93) (94, 94) (95, 95) (96, 96) (97, 97) (98, 98) (99, 99) (100, 100) (101, 101) (102, 102) (103, 103) (104, 104) (105, 105)
(106, 106) (107, 107) (108, 108) (109, 109) (110, 110) (111, 111) (112, 112) (113, 113) (114, 114) (115, 115) (116, 116) (117, 117) (1
18, 118) (119, 119) (120, 120) (121, 121) (122, 122) (123, 123) (124, 124) (125, 125) (126, 126) (127, 127) (128, 128) (129, 129) (130,
130) (131, 131) (132, 132) (133, 133) (134, 134) (135, 135) (136, 136) (137, 137) (138, 138) (139, 139) (140, 140) (141, 141) (142, 14
2) (143, 143) (144, 144) (145, 145) (146, 146) (147, 147) (148, 148) (149, 149) (150, 150) (151, 151) (152, 152) (153, 153) (154, 154)
(155, 155) (156, 156) (157, 157) (158, 158) (159, 159) (160, 160) (161, 161) (162, 162) (163, 163) (164, 164) (165, 165) (166, 166) (16
7, 167) (168, 168) (169, 169) (170, 170) (171, 171) (172, 172) (173, 173) (174, 174) (175, 175) (176, 176) (177, 177) (178, 178) (179,
179) (180, 180) (181, 181) (182, 182) (183, 183) (184, 184) (185, 185) (186, 186) (187, 187) (188, 188) (189, 189) (190, 190) (191, 191
) (192, 192) (193, 193) (194, 194) (195, 195) (196, 196) (197, 197) (198, 198) (199, 199) (200, 200) (201, 201) (202, 202) (203, 203) (
204, 204) (205, 205) (206, 206) (207, 207) (208, 208) (209, 209) (210, 210) (211, 211) (212, 212)
Traceback (most recent call last):
(Local_id, Segment_id)
(0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (1
7, 17) (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) (27, 27) (28, 28) (29, 29) (30, 30) (31, 31) (3
2, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, 38) (39, 39) (40, 40) (41, 41) (42, 42) (43, 43) (44, 44) (45, 45) (46, 46) (4
7, 47) (48, 48) (49, 49) (50, 50) (51, 51) (52, 52) (53, 53) (54, 54) (55, 55) (56, 56) (57, 57) (58, 58) (59, 59) (60, 60) (61, 61) (6
2, 62) (63, 63) (64, 64) (65, 65) (66, 66) (67, 67) (68, 68) (69, 69) (70, 70) (71, 71) (72, 72) (73, 73) (74, 74) (75, 75) (76, 76) (7
7, 77) (78, 78) (79, 79) (80, 80) (81, 81) (82, 82) (83, 83) (84, 84) (85, 85) (86, 86) (87, 87) (88, 88) (89, 89) (90, 90) (91, 91) (9
2, 92) (93, 93) (94, 94) (95, 95) (96, 96) (97, 97) (98, 98) (99, 99) (100, 100) (101, 101) (102, 102) (103, 103) (104, 104) (105, 105)
(106, 106) (107, 107) (108, 108) (109, 109) (110, 110) (111, 111) (112, 112) (113, 113) (114, 114) (115, 115) (116, 116) (117, 117) (1
18, 118) (119, 119) (120, 120) (121, 121) (122, 122) (123, 123) (124, 124) (125, 125) (126, 126) (127, 127) (128, 128) (129, 129) (130,
130) (131, 131) (132, 132) (133, 133) (134, 134) (135, 135) (136, 136) (137, 137) (138, 138) (139, 139) (140, 140) (141, 141) (142, 14
2) (143, 143) (144, 144) (145, 145) (146, 146) (147, 147) (148, 148) (149, 149) (150, 150) (151, 151) (152, 152) (153, 153) (154, 154)
(155, 155) (156, 156) (157, 157) (158, 158) (159, 159) (160, 160) (161, 161) (162, 162) (163, 163) (164, 164) (165, 165) (166, 166) (16
7, 167) (168, 168) (169, 169) (170, 170) (171, 171) (172, 172) (173, 173) (174, 174) (175, 175) (176, 176) (177, 177) (178, 178) (179,
179) (180, 180) (181, 181) (182, 182) (183, 183) (184, 184) (185, 185) (186, 186) (187, 187) (188, 188) (189, 189) (190, 190) (191, 191
) (192, 192) (193, 193) (194, 194) (195, 195) (196, 196) (197, 197) (198, 198) (199, 199) (200, 200) (201, 201) (202, 202) (203, 203) (
204, 204) (205, 205) (206, 206) (207, 207) (208, 208) (209, 209) (210, 210) (211, 211) (212, 212)
Traceback (most recent call last):
File "/home/andrean/spring_v0-84-1470/bin/segmentexam_mpi", line 152, in <module>
sys.exit(spring.segment2d.segmentexam_mpi.main())
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py",
line 175, in main
stack.add_up_power_spectra()
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py",
line 153, in add_up_power_spectra
segment_ids = self.prepare_segmentexam_mpi()
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam_mpi.py",
line 52, in prepare_segmentexam_mpi
self.infilestack, self.segsizepix, self.helixwidthpix, self.pixelsize, segment_ids, binned_stack)
File "/home/andrean/spring_v0-84-1470/lib/python2.7/site-packages/emspring-0.84.1470-py2.7.egg/spring/segment2d/segmentexam.py", line
200, in apply_binfactor
helixwidthpix = helixwidthpix/binfactor
ZeroDivisionError: integer division or modulo by zero
Rank 0 on machine cryo2.ps.local.nimr with process ID 2847 raised an error message. Find the corresponding error message above. All oth
er MPI processes are aborted. Ignore the error messages thereafter as they can arise as a result of the aborting procedure.
INFO:CPU5:bin_image_stack_by_binfactor:The following segments were binned by a factor 0 for further analysis and saved in /tmp/andrean-
25_Feb_2016_17_16_31-2891/flu_4class.hdf.
(Local_id, Segment_id)
(0, 1063) (1, 1064) (2, 1065) (3, 1066) (4, 1067) (5, 1068) (6, 1069) (7, 1070) (8, 1071) (9, 1072) (10, 1073) (11, 1074) (12, 1075) (1
3, 1076) (14, 1077) (15, 1078) (16, 1079) (17, 1080) (18, 1081) (19, 1082) (20, 1083) (21, 1084) (22, 1085) (23, 1086) (24, 1087) (25,
1088) (26, 1089) (27, 1090) (28, 1091) (29, 1092) (30, 1093) (31, 1094) (32, 1095) (33, 1096) (34, 1097) (35, 1098) (36, 1099) (37, 110
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, 1125) (63, 1126) (64, 1127) (65, 1128) (66, 1129) (67, 1130) (68, 1131) (69, 1132) (70, 1133) (71, 1134) (72, 1135) (73, 1136) (74, 1
137) (75, 1138) (76, 1139) (77, 1140) (78, 1141) (79, 1142) (80, 1143) (81, 1144) (82, 1145) (83, 1146) (84, 1147) (85, 1148) (86, 1149
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(133, 1196) (134, 1197) (135, 1198) (136, 1199) (137, 1200) (138, 1201) (139, 1202) (140, 1203) (141, 1204) (142, 1205) (143, 1206) (1
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(178, 1241) (179, 1242) (180, 1243) (181, 1244) (182, 1245) (183, 1246) (184, 1247) (185, 1248) (186, 1249) (187, 1250) (188, 1251) (1
89, 1252) (190, 1253) (191, 1254) (192, 1255) (193, 1256) (194, 1257) (195, 1258) (196, 1259) (197, 1260) (198, 1261) (199, 1262) (200,
1263) (201, 1264) (202, 1265) (203, 1266) (204, 1267) (205, 1268) (206, 1269) (207, 1270) (208, 1271) (209, 1272) (210, 1273) (211, 12
74) (212, 1275)
INFO:andrean:/home/andrean/spring_v0-84-1470/parts/openmpi/bin/mpirun -np 6 /home/andrean/spring_v0-84-1470/bin/springenv /home/andrean
/spring_v0-84-1470/bin/python cleanup.py
er MPI processes are aborted. Ignore the error messages thereafter as they can arise as a result of the aborting procedure.
INFO:CPU5:bin_image_stack_by_binfactor:The following segments were binned by a factor 0 for further analysis and saved in /tmp/andrean-
25_Feb_2016_17_16_31-2891/flu_4class.hdf.
(Local_id, Segment_id)
(0, 1063) (1, 1064) (2, 1065) (3, 1066) (4, 1067) (5, 1068) (6, 1069) (7, 1070) (8, 1071) (9, 1072) (10, 1073) (11, 1074) (12, 1075) (1
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1088) (26, 1089) (27, 1090) (28, 1091) (29, 1092) (30, 1093) (31, 1094) (32, 1095) (33, 1096) (34, 1097) (35, 1098) (36, 1099) (37, 110
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1263) (201, 1264) (202, 1265) (203, 1266) (204, 1267) (205, 1268) (206, 1269) (207, 1270) (208, 1271) (209, 1272) (210, 1273) (211, 12
74) (212, 1275)
INFO:andrean:/home/andrean/spring_v0-84-1470/parts/openmpi/bin/mpirun -np 6 /home/andrean/spring_v0-84-1470/bin/springenv /home/andrean
/spring_v0-84-1470/bin/python cleanup.py
Carsten Sachse
Mar 1, 2016, 4:08:14 PM3/1/16
to emspring
Dear Andrea,
Thank you for the parameters.
First, you're using a pixel size of 7.0.
SEGMENTEXAM is not getting the following critical parameter:
Power spectrum resolution cutoff in 1/Angstrom = None
Therefore, SPRING will revert to the default value 0.15, i.e. 1/6.67 Angstrom.
Your highest possible resolution, however, is 14 Angstrom with that given pixel size.
SEGMENTEXAM computes an internal bin factor in the following way:
binfactor = int(round(1/(self.rescutoff*self.pixelsize*2)))
According to this calculation the binfactor becomes 0, which causes the error. Therefore, in order to prevent this error, you will need to provide the following parameter:
Power spectrum resolution cutoff in 1/Angstrom = 0.07
The future fix will prevent this behavior. Thank you for posting your questions.
Best wishes,
Carsten
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