INFO 2025-06-26 12:27:58,032 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 12:27:58,033 process.py process_mission():434 [1] dorado_info[mission]["comment"] = BIOLUME mission - Filled sensors with sand half-way through survey at 17m; data after that is bad Got 'Error in plot_sections (line 852)' when reprocessing attempted on 30 May 2018 - ctdToUse = ctd1 INFO 2025-06-26 12:27:58,033 process.py process_mission():449 [1] Processing BIOLUME mission 2007.029.11 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:27:58,033 process.py download_process():165 [1] Download and processing steps for 2007.029.11 INFO 2025-06-26 12:27:58,033 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007029/2007.029.11 INFO 2025-06-26 12:27:58,033 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007029/2007.029.11 to /data/auv_data/dorado/missionlogs/2007.029.11 INFO 2025-06-26 12:28:03,592 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.029.11 INFO 2025-06-26 12:28:03,592 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/ctdDriver.log (25461699 bytes) INFO 2025-06-26 12:28:05,437 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.029.11/ctdDriver.log: [ 6 15 32 750 1645 1801 3360 5377 5547 6695 7608 8550 10376 10629 11771 14625 20639 26656 27067 40940 100504 107058 125758 126681 136035 139366 154388 159053 182905 198082 211857 230634 239342 257902 281795 287905 288371] INFO 2025-06-26 12:28:05,521 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/ctdDriver2.log (25463013 bytes) INFO 2025-06-26 12:28:07,331 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.029.11/ctdDriver2.log: [ 22 651 841 2764 3441 6681 8538 11253 19292 22319 25595 33788 35541 40942 49200 64523 78062 87402 97934 106832 112542 115505 138153 146205 147485 152162 154402 154657 159765 159852 196606 197918 211874 239358 250412 250498 257917 279005 281810 287920] INFO 2025-06-26 12:28:07,417 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/gps.log (115412 bytes) INFO 2025-06-26 12:28:07,437 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/hydroscatlog.log (17372654 bytes) INFO 2025-06-26 12:28:09,462 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.029.11/hydroscatlog.log: [ 3 66 240 307 505 561 784 810 1017 1051 1126 1128 1628 1631 1707 1874 1921 2087 2240 2291 2303 2304 2388 2438 2594 3280 3446 4171 5167 5339 6448 6762 7122 7589 7746 7747 8622 9208 10448 10701 11337 11882 12063 12080 13733 14576 15963 16980 17868 19064 23801 25429 26751 27161 28891 31093 35634 40589 40779 41742 42428 44229 48191 52816 54017 54144 54412 55687 59926 63943 64641 72281 77106 78185 80869 86597 87579 87803 93179 94294 95483 98093 100676 101008 107293 110955 111668 112368 113804 114440 125630 127863 130664 131041 134573 138151 138162 141776 142186 148002 151091 154616 154714 166482 166593 168137 174848 177138 178688 182674 182872 183216 183217 183910 190643 194980 196828 202141 203422 207040 209254 212091 214686 220629 230858 234243 243116 251913 259022 262099 265607 268811 273102 278504 281996 288096 288570 288946] INFO 2025-06-26 12:28:09,506 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/navigation.log (85341266 bytes) INFO 2025-06-26 12:28:15,717 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/isuslog.log (1630069 bytes) INFO 2025-06-26 12:28:15,889 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.029.11/isuslog.log: [1 3 4 5 6 7 8] INFO 2025-06-26 12:28:15,894 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/parosci.log (37272038 bytes) INFO 2025-06-26 12:28:18,959 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.029.11/parosci.log: [ 3 5 16 17 19 20 63 277 278 325 326 331 332 358 359 361 850 852 893 895 1317 1318 1381 1382 1383 1470 1471 2223 2224 2469 2470 2748 2836 2930 2931 2951 2952 2954 3039 3040 3041 3557 3558 4112 4197 4384 4385 4386 4387 4588 4589 4590 5006 5008 5043 5045 5167 5875 5876 5877 6955 7562 7563 7609 7610 8488 8489 8969 8971 8972 9113 9114 9115 9232 9233 9234 10041 11172 11173 11174 11471 12929 12930 13176 13635 13840 13842 13843 13973 13975 14474 14573 15028 16571 16573 16574 19081 20330 20331 20333 20576 20577 20752 20753 20754 21656 21657 21776 21777 24669 28672 30956 30957 30959 31120 31121 31122 32001 32002 32003 32358 32360 33243 35752 36792 37172 37173 39406 44449 47867 47869 49111 49112 51076 51077 51911 55668 55669 58659 58660 65293 65892 66691 68812 71692 74474 74475 74476 74875 76476 76477 76478 77425 77426 77427 83334 84373 88940 88941 95511 96463 107477 107478 107479 108807 109316 111901 114570 114572 114573 115656 115657 115658 118565 118567 129193 141604 141605 144830 144831 144833 149307 149309 162256 162257 162259 167026 168007 168008 169430 169431 171466 172411 172486 172487 172488 179771 180860 182117 189558 191601 191602 191603 198853 198854 198874 198875 199217 199219 205947 205948 205950 206794 208466 208467 208468 209696 209697 217931 229795 229796 229797 232264 234897 234898 237328 237329 249637 249638 249640 249641 249926 249927 250397 250399 252124 252125 252126 252127 252919 252920 252921 256112 275195 275196 275366 275367 287646 287807 290171 290172 290173 293329 293331 294288 297634 297635 297636 299545 299546 302351 302352 302354 302355 305277 305278 305280 324999 325000 330420 330422 330423 332459 332460 332461 343006 343007 350528 361011 361012 361013 363564 367674 370606 370607 380709 381164 389667 389668 390738 390739 390740 391232 391233 396185 396186 410832 410833 410834 413383 413384 413385 415005 415006 424400 427521 427794 427796 427797 430941 430942 446564 446565 446859 446860 446861 448220 448221 451046 451047 462964 462965 465923 465924 465925 468091 468092 468093 468998 471148 475137 479297 479298 479299 489981 489982 489983 491428 491430 491431 493289 493290 493292 504049 504051 504052 504986 511782 511783 511784 522977 522979 527931 527932 531447 531449 531934 542182 545614 545616 545617 551547 551549 555318 555319 555473 555474 555475 558986 561252 571656 575821 575823 575824 576975 576977 576978 580314 580315 583783 583784 583786 591759 594977 599163 599165 599166 599383 599384 619186 619187 619189 619331 621062 621064 621065 642530 642531 642853 642855 656572 656573 656574 666960 666961 669122 672384 672630 675633 675634 675635 675636 675645 675646 675647 677577 684909 684911 684962 684964 684965 692272 694703 694704 710911 710912 712369 712370 720955 720956 746947 746948 746949 751885 751887 769559 770944 771360 771361 771363 772658 772680 772681 772682 773925 773926 774935] INFO 2025-06-26 12:28:19,059 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/tailCone.log (17348443 bytes) INFO 2025-06-26 12:28:21,209 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.029.11/biolume.log (19704364 bytes) INFO 2025-06-26 12:28:23,101 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:28:24,090 logs2netcdfs.py download_process_logs():807 [1] Time to process: 20.50 seconds WARNING 2025-06-26 12:28:24,090 process.py download_process():196 [1] No lopc.bin file for 2007.029.11 INFO 2025-06-26 12:28:24,090 process.py calibrate():227 [1] Calibration steps for 2007.029.11 INFO 2025-06-26 12:28:24,634 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 12:28:24,636 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:28:25,432 calibrate.py _nudge_pos():1806 [1] 104: 0.180 -0.0006014 -0.0001248 2318 7.83 -11.412 -2.953 2007-01-29T21:27:53.894359552 INFO 2025-06-26 12:28:26,082 calibrate.py _nudge_pos():1806 [1] 168: 0.180 -0.0038028 0.0000082 9760 32.65 -17.313 0.047 2007-01-29T22:01:35.895843072 INFO 2025-06-26 12:28:26,644 calibrate.py _nudge_pos():1806 [1] 223: 0.190 -0.0041844 -0.0001772 10183 34.00 -18.299 -0.966 2007-01-29T22:36:29.892394496 INFO 2025-06-26 12:28:27,313 calibrate.py _nudge_pos():1806 [1] 288: 0.180 -0.0032969 0.0001724 9272 30.93 -15.852 1.033 2007-01-29T23:08:29.900864768 INFO 2025-06-26 12:28:27,772 calibrate.py _nudge_pos():1806 [1] 333: 0.180 -0.0011919 -0.0006227 8019 26.76 -6.622 -4.312 2007-01-29T23:35:59.897832448 INFO 2025-06-26 12:28:28,294 calibrate.py _nudge_pos():1806 [1] 384: 0.190 -0.0023532 -0.0010144 13748 45.86 -7.627 -4.098 2007-01-30T00:22:41.895882496 INFO 2025-06-26 12:28:28,755 calibrate.py _nudge_pos():1806 [1] 429: 0.190 -0.0022562 -0.0010768 13211 44.06 -7.609 -4.528 2007-01-30T01:07:29.891741952 INFO 2025-06-26 12:28:29,108 calibrate.py _nudge_pos():1806 [1] 462: 0.200 -0.0006029 -0.0003597 13482 44.96 -1.992 -1.483 2007-01-30T01:52:59.894723840 INFO 2025-06-26 12:28:29,549 calibrate.py _nudge_pos():1806 [1] 504: 0.010 -0.0022044 0.0001475 13765 45.91 -7.130 0.595 2007-01-30T02:39:36.093171200 INFO 2025-06-26 12:28:30,116 calibrate.py _nudge_pos():1806 [1] 558: 0.200 -0.0035214 0.0001518 11668 38.91 -13.437 0.723 2007-01-30T03:19:23.899595264 INFO 2025-06-26 12:28:30,515 calibrate.py _nudge_pos():1806 [1] 596: 0.010 -0.0014939 -0.0000856 3769 12.58 -17.631 -1.261 2007-01-30T03:32:36.095326208 INFO 2025-06-26 12:28:31,010 calibrate.py _nudge_pos():1806 [1] 643: 0.010 -0.0032803 0.0017081 11789 39.33 -12.379 8.048 2007-01-30T04:12:42.100503552 INFO 2025-06-26 12:28:31,485 calibrate.py _nudge_pos():1806 [1] 688: 0.010 -0.0011920 0.0013278 9433 31.46 -5.622 7.820 2007-01-30T04:44:54.098152704 INFO 2025-06-26 12:28:31,890 calibrate.py _nudge_pos():1806 [1] 726: 0.020 -0.0019360 0.0027596 13776 45.98 -6.246 11.121 2007-01-30T05:31:30.096613632 INFO 2025-06-26 12:28:32,457 calibrate.py _nudge_pos():1806 [1] 779: 0.020 -0.0021868 0.0033021 13654 45.53 -7.122 13.439 2007-01-30T06:17:54.095896576 INFO 2025-06-26 12:28:33,049 calibrate.py _nudge_pos():1806 [1] 834: 0.020 -0.0022356 0.0047833 13270 44.26 -7.487 20.024 2007-01-30T07:03:06.100111360 INFO 2025-06-26 12:28:33,648 calibrate.py _nudge_pos():1806 [1] 888: 0.030 -0.0041927 0.0038723 13166 43.91 -14.147 16.340 2007-01-30T07:47:54.095971328 INFO 2025-06-26 12:28:34,277 calibrate.py _nudge_pos():1806 [1] 945: 0.030 -0.0024518 0.0027033 10659 35.56 -10.213 14.085 2007-01-30T08:24:24.095945984 INFO 2025-06-26 12:28:34,901 calibrate.py _nudge_pos():1806 [1] 1001: 0.030 -0.0004218 0.0007365 3804 12.68 -4.927 10.763 2007-01-30T08:38:00.100045824 INFO 2025-06-26 12:28:35,599 calibrate.py _nudge_pos():1806 [1] 1064: 0.030 0.0013762 0.0014588 7695 25.66 7.943 10.533 2007-01-30T09:04:42.100301312 INFO 2025-06-26 12:28:36,048 calibrate.py _nudge_pos():1806 [1] 1104: 0.040 -0.0021505 0.0025928 9581 31.95 -9.971 15.039 2007-01-30T09:37:18.096306432 INFO 2025-06-26 12:28:36,501 calibrate.py _nudge_pos():1806 [1] 1145: 0.040 -0.0017368 0.0006700 17068 56.93 -4.520 2.181 2007-01-30T10:34:54.099554048 INFO 2025-06-26 12:28:36,525 calibrate.py _nudge_pos():1806 [1] 1147: 0.040 0.0000580 -0.0000133 45 0.15 58.596 -16.847 2007-01-30T10:35:04.098868992 INFO 2025-06-26 12:28:36,961 calibrate.py _nudge_pos():1806 [1] 1186: 0.040 -0.0026738 0.0013016 14571 48.60 -8.154 4.963 2007-01-30T11:24:18.096506368 INFO 2025-06-26 12:28:37,467 calibrate.py _nudge_pos():1806 [1] 1232: 0.050 -0.0046592 0.0028051 18184 60.65 -11.390 8.571 2007-01-30T12:25:42.094135040 INFO 2025-06-26 12:28:38,089 calibrate.py _nudge_pos():1806 [1] 1288: 0.050 -0.0034799 0.0040981 17084 56.98 -9.057 13.327 2007-01-30T13:23:36.096149760 INFO 2025-06-26 12:28:38,587 calibrate.py _nudge_pos():1806 [1] 1331: 0.060 -0.0011461 0.0015956 7916 26.40 -6.440 11.201 2007-01-30T13:50:42.094761216 INFO 2025-06-26 12:28:39,059 calibrate.py _nudge_pos():1806 [1] 1372: 0.060 -0.0041851 0.0049047 13025 43.43 -14.297 20.927 2007-01-30T14:34:48.093497856 INFO 2025-06-26 12:28:39,105 calibrate.py _nudge_pos():1806 [1] 1376: 0.070 -0.0000524 0.0000034 40 0.13 -59.748 4.879 2007-01-30T14:34:59.092744448 INFO 2025-06-26 12:28:39,562 calibrate.py _nudge_pos():1806 [1] 1417: 0.070 -0.0039905 0.0020145 14457 48.23 -12.279 7.740 2007-01-30T15:23:53.091751680 INFO 2025-06-26 12:28:40,122 calibrate.py _nudge_pos():1806 [1] 1464: 0.060 -0.0052617 -0.0001243 13240 44.15 -17.694 -0.522 2007-01-30T16:08:48.097131008 INFO 2025-06-26 12:28:40,621 calibrate.py _nudge_pos():1806 [1] 1508: 0.070 0.0027444 -0.0017494 12977 43.28 9.415 -7.490 2007-01-30T16:52:48.096278784 INFO 2025-06-26 12:28:41,140 calibrate.py _nudge_pos():1806 [1] 1547: 0.080 0.0005171 -0.0027105 9373 31.26 2.456 -16.066 2007-01-30T17:24:42.095161088 INFO 2025-06-26 12:28:41,623 calibrate.py _nudge_pos():1862 [1] 1557: - - - 1 0.00 - - INFO 2025-06-26 12:28:41,623 calibrate.py _nudge_pos():1868 [1] Points in final series = 361492 WARNING 2025-06-26 12:28:54,269 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:29:32,439 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:29:52,999 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:29:55,175 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:29:55,179 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.029.11/ctd1.nc WARNING 2025-06-26 12:29:55,183 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (126337) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 12:29:55,184 calibrate.py _range_qc_combined_nc():898 [1] Setting 126337 ctd1_salinity values to NaN INFO 2025-06-26 12:29:55,185 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 12:29:55,185 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:30:11,166 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 21 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:30:13,309 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 21 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:30:13,314 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.029.11/ctd2.nc WARNING 2025-06-26 12:30:13,318 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (126201) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 12:30:13,318 calibrate.py _range_qc_combined_nc():898 [1] Setting 126201 ctd2_salinity values to NaN INFO 2025-06-26 12:30:13,319 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 12:30:13,319 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:30:15,750 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:30:19,092 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4345506 4345507 4345508] INFO 2025-06-26 12:30:19,751 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:30:19,758 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 12:30:19,759 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.029.11 ERROR 2025-06-26 12:30:19,759 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.029.11 INFO 2025-06-26 12:30:20,123 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_cal.nc INFO 2025-06-26 12:30:42,708 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 12:30:42,712 process.py align():251 [1] Alignment steps for 2007.029.11 INFO 2025-06-26 12:30:42,759 align.py process_cal():139 [1] Processing dorado_2007.029.11_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.029.11 INFO 2025-06-26 12:30:42,864 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:30:42,874 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:30:43,122 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:30:43,138 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:30:43,360 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:30:43,373 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:30:43,512 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:30:43,512 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:30:43,609 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:30:43,623 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:30:43,839 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:30:43,850 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:44,044 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:30:44,054 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:44,244 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:30:44,254 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:44,444 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:44,454 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:44,648 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:44,658 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:44,847 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:44,857 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:45,051 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:45,061 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:45,250 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:45,261 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:45,452 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:45,462 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:45,651 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:45,665 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:45,857 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:45,867 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:46,060 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:46,070 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:46,260 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:46,270 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:46,463 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:46,474 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:46,667 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:46,679 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:46,872 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:46,885 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:47,082 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:47,092 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:47,288 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:47,299 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:47,491 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:47,501 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:47,690 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.029.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:30:47,700 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:30:47,942 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:30:48,098 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:30:48,254 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:30:48,413 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:30:48,586 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:30:48,731 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_align.nc INFO 2025-06-26 12:30:48,897 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 12:30:48,899 process.py resample():273 [1] Resampling steps for 2007.029.11 INFO 2025-06-26 12:30:48,899 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:30:48,935 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_align.nc mission netCDF file INFO 2025-06-26 12:30:48,945 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_align.nc mission netCDF file INFO 2025-06-26 12:30:48,947 resample.py get_mission_start_end():1145 [1] navigation: 2007-01-29T21:18:54.971278336 to 2007-01-30T17:25:25.292201728 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 12:30:48,950 resample.py get_mission_start_end():1145 [1] hs2 : 2007-01-29T21:18:27.273175808 to 2007-01-30T17:25:25.342198272 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 12:30:48,953 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-01-29T21:18:42.392140032 to 2007-01-30T17:25:25.372196096 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:30:48,956 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-01-29T21:18:44.791975680 to 2007-01-30T17:25:25.362196992 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 12:30:48,957 resample.py get_mission_start_end():1145 [1] isus : 2007-01-29T21:19:23.119350272 to 2007-01-30T17:25:21.542458624 (0 days 00:00:03.829737472 before mission_end) INFO 2025-06-26 12:30:48,959 resample.py get_mission_start_end():1145 [1] biolume : 2007-01-29T21:18:21.243554560 to 2007-01-30T17:25:23.912261888 (0 days 00:00:01.459934208 before mission_end) INFO 2025-06-26 12:30:48,962 resample.py get_mission_start_end():1145 [1] tailcone : 2007-01-29T21:18:22.363512064 to 2007-01-30T17:25:25.342198272 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 12:30:48,963 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_align.nc mission netCDF file INFO 2025-06-26 12:30:48,963 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:49,712 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:49,828 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:49,941 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,056 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,153 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,251 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,347 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,442 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,534 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,871 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:50,962 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,054 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,144 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,234 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,324 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,417 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,514 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,611 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:51,963 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,057 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,152 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,246 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,280 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,309 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,336 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,369 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,477 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:30:52,999 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_1S.nc INFO 2025-06-26 12:30:54,925 create_products.py gulper_odv():401 [1] No gulper times found for 2007.029.11 INFO 2025-06-26 12:30:54,926 process.py archive():337 [1] Archiving steps for 2007.029.11 INFO 2025-06-26 12:30:54,926 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11, BASE_PATH = /data/auv_data INFO 2025-06-26 12:30:54,927 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:30:54,929 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.029.11_1S.nc INFO 2025-06-26 12:30:54,987 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:30:54,989 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.029.11_cal.nc INFO 2025-06-26 12:30:55,276 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:30:55,278 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.029.11_align.nc INFO 2025-06-26 12:30:55,555 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:30:55,634 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:55,713 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:55,719 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:55,772 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:56,004 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:56,016 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:56,115 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:56,177 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:56,367 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007029/2007.029.11 done. INFO 2025-06-26 12:30:56,368 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:30:56,368 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.029.11/dorado_2007.029.11_processing.log /Volumes/AUVCTD/surveys/2007/netcdf