INFO 2025-10-20 23:25:22,145 process.py process_mission():429 [1] commandline = /src/data/process_i2map.py -v --noinput --start_year 2019 --end_year 2019 --start_yd 1 --end_yd 365 --num_cores 1 --clobber INFO 2025-10-20 23:25:22,145 process.py process_mission():449 [1] Processing i2map mission 2019.311.00 by user docker_user on host bc943cff5f21 INFO 2025-10-20 23:25:22,145 process.py download_process():165 [1] Download and processing steps for 2019.311.00 INFO 2025-10-20 23:25:22,145 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/M3/master/i2MAP/2019/11/20191107/2019.311.00 INFO 2025-10-20 23:25:22,145 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/M3/master/i2MAP/2019/11/20191107/2019.311.00 to /data/auv_data/i2map/missionlogs/2019.311.00 INFO 2025-10-20 23:25:23,630 logs2netcdfs.py download_process_logs():779 [1] Processing mission: i2map 2019.311.00 INFO 2025-10-20 23:25:23,630 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.311.00/gps.log (460004 bytes) INFO 2025-10-20 23:25:23,684 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2019.311.00/gps.log: [ 440 441 2701 3682 3683] INFO 2025-10-20 23:25:23,686 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.311.00/navigation.log (144838464 bytes) INFO 2025-10-20 23:25:33,751 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2019.311.00/navigation.log: [ 17599 17600 17601 17602 17603 17604 17605 17606 17607 17608 30730 30731 30732 30733 30734 30735 30736 30737 30738 30739 30740 44376 44377 44378 44379 44380 44381 44382 44383 44384 44385 58097 58098 58099 58100 58101 58102 58103 58104 58105 58106 58107 72323 72324 72325 72326 72327 72328 72329 72330 72331 72332 72333 89884 89885 89886 89887 89888 89889 89890 89891 89892 89893 104085 104086 104087 104088 104089 104090 104091 104092 104093 104094 117056 117057 117058 117059 117060 117061 117062 117063 117064 117065 130122 130123 130124 130125 130126 130127 130128 130129 130130 130131 143058 143059 143060 143061 143062 143063 143064 143065 143066 143067 143068 156609 156610 156611 156612 156613 156614 156615 156616 156617 156618 169565 169566 169567 169568 169569 169570 169571 169572 169573 169574 183746 183747 183748 183749 183750 183751 183752 183753 183754 183755 197202 197203 197204 197205 197206 197207 197208 197209 197210 197211 197212 211508 211509 211510 211511 211512 211513 211514 211515 211516 211517 211518 225744 225745 225746 225747 225748 225749 225750 225751 225752 225753 239395 239396 239397 239398 239399 239400 239401 239402 239403 239404 246561 246562 246563 246564 246565 266597 266598 266599 266600 266601 266602 266603 266604 266605 266606 279568 279569 279570 279571 279572 279573 279574 279575 279576 279577 279578 310610 310611 310612 310613 310614 324201 324202 324203 324204 324205 324206 324207 324208 324209 324210 337697 337698 337699 337700 337701 337702 337703 337704 337705 337706 351248 351249 351250 351251 351252 351253 351254 351255 351256 351257 364139 364140 364141 364142 364143 364144 364145 364146 364147 364148 377805 377806 377807 377808 377809 377810 377811 377812 377813 377814 377815 391446 391447 391448 391449 391450 391451 391452 391453 391454 391455 405027 405028 405029 405030 405031 405032 405033 405034 405035 405036 418748 418749 418750 418751 418752 418753 418754 418755 418756 418757] INFO 2025-10-20 23:25:34,426 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.311.00/parosci.log (40710710 bytes) INFO 2025-10-20 23:25:37,701 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2019.311.00/parosci.log: [ 35278 35279 35280 35281 35282 35283 35284 35285 35286 35287 35288 35289 35290 35291 35292 35293 35294 35295 35296 35297 35298 61413 61414 61415 61416 61417 61418 61419 61420 61421 61422 61423 61424 61425 61426 61427 61428 61429 61430 61431 61432 61433 88574 88575 88576 88577 88578 88579 88580 88581 88582 88583 88584 88585 88586 88587 88588 88589 88590 88591 88592 88593 88594 115882 115883 115884 115885 115886 115887 115888 115889 115890 115891 115892 115893 115894 115895 115896 115897 115898 115899 115900 115901 115902 144200 144201 144202 144203 144204 144205 144206 144207 144208 144209 144210 144211 144212 144213 144214 144215 144216 144217 144218 144219 144220 144221 179153 179154 179155 179156 179157 179158 179159 179160 179161 179162 179163 179164 179165 179166 179167 179168 179169 179170 179171 179172 179173 207419 207420 207421 207422 207423 207424 207425 207426 207427 207428 207429 207430 207431 207432 207433 207434 207435 207436 207437 207438 207439 233236 233237 233238 233239 233240 233241 233242 233243 233244 233245 233246 233247 233248 233249 233250 233251 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421243 421244 421245 421246 421247 421248 421249 421250 421251 449567 449568 449569 449570 449571 449572 449573 449574 449575 449576 449577 449578 449579 449580 449581 449582 449583 449584 449585 449586 449587 476739 476740 476741 476742 476743 476744 476745 476746 476747 476748 476749 476750 476751 476752 476753 476754 476755 476756 476757 476758 476759 491002 491003 491004 491005 491006 491007 491008 491009 491010 491011 491012 530883 530884 530885 530886 530887 530888 530889 530890 530891 530892 530893 530894 530895 530896 530897 530898 530899 530900 530901 530902 530903 556701 556702 556703 556704 556705 556706 556707 556708 556709 556710 556711 556712 556713 556714 556715 556716 556717 556718 556719 556720 556721 556722 556842 618488 618489 618490 618491 618492 618493 618494 618495 618496 618497 618498 645540 645541 645542 645543 645544 645545 645546 645547 645548 645549 645550 645551 645552 645553 645554 645555 645556 645557 645558 645559 645560 672403 672404 672405 672406 672407 672408 672409 672410 672411 672412 672413 672414 672415 672416 672417 672418 672419 672420 672421 672422 672423 699374 699375 699376 699377 699378 699379 699380 699381 699382 699383 699384 699385 699386 699387 699388 699389 699390 699391 699392 699393 699394 725032 725033 725034 725035 725036 725037 725038 725039 725040 725041 725042 725043 725044 725045 725046 725047 725048 725049 725050 725051 725052 752232 752233 752234 752235 752236 752237 752238 752239 752240 752241 752242 752243 752244 752245 752246 752247 752248 752249 752250 752251 752252 779383 779384 779385 779386 779387 779388 779389 779390 779391 779392 779393 779394 779395 779396 779397 779398 779399 779400 779401 779402 779403 806414 806415 806416 806417 806418 806419 806420 806421 806422 806423 806424 806425 806426 806427 806428 806429 806430 806431 806432 806433 806434 833724 833725 833726 833727 833728 833729 833730 833731 833732 833733 833734 833735 833736 833737 833738 833739 833740 833741 833742 833743 833744] INFO 2025-10-20 23:25:37,819 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.311.00/seabird25p.log (4511170 bytes) INFO 2025-10-20 23:25:38,121 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2019.311.00/seabird25p.log: [ 1 28316 28317 28318 28319 28320 28321 28322 28323 28324 28325 28326 28327 28328 28329 28330 28331 28332] INFO 2025-10-20 23:25:38,139 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2019.311.00/tailCone.log (20447755 bytes) INFO 2025-10-20 23:25:40,547 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2019.311.00/tailCone.log: [ 17767 17768 17769 17770 17771 17772 17773 17774 17775 17776 17777 30897 30898 30899 30900 30901 30902 30903 30904 30905 30906 30907 44543 44544 44545 44546 44547 44548 44549 44550 44551 44552 58265 58266 58267 58268 58269 58270 58271 58272 58273 58274 58275 72491 72492 72493 72494 72495 72496 72497 72498 72499 72500 72501 90052 90053 90054 90055 90056 90057 90058 90059 90060 90061 90062 104252 104253 104254 104255 104256 104257 104258 104259 104260 104261 117222 117223 117224 117225 117226 117227 117228 117229 117230 117231 130288 130289 130290 130291 130292 130293 130294 130295 130296 130297 143224 143225 143226 143227 143228 143229 143230 143231 143232 143233 143234 156775 156776 156777 156778 156779 156780 156781 156782 156783 156784 169731 169732 169733 169734 169735 169736 169737 169738 169739 169740 183912 183913 183914 183915 183916 183917 183918 183919 183920 183921 183922 197368 197369 197370 197371 197372 197373 197374 197375 197376 197377 211673 211674 211675 211676 211677 211678 211679 211680 211681 211682 211683 225909 225910 225911 225912 225913 225914 225915 225916 225917 225918 239560 239561 239562 239563 239564 239565 239566 239567 239568 239569 239570 246726 246727 246728 246729 246730 266761 266762 266763 266764 266765 266766 266767 266768 266769 266770 279732 279733 279734 279735 279736 279737 279738 279739 279740 279741 279742 310773 310774 310775 310776 310777 324364 324365 324366 324367 324368 324369 324370 324371 324372 324373 337860 337861 337862 337863 337864 337865 337866 337867 337868 337869 351410 351411 351412 351413 351414 351415 351416 351417 351418 351419 364301 364302 364303 364304 364305 364306 364307 364308 364309 364310 377967 377968 377969 377970 377971 377972 377973 377974 377975 377976 377977 391607 391608 391609 391610 391611 391612 391613 391614 391615 391616 405188 405189 405190 405191 405192 405193 405194 405195 405196 405197 418909 418910 418911 418912 418913 418914 418915 418916 418917 418918] INFO 2025-10-20 23:25:40,596 logs2netcdfs.py download_process_logs():807 [1] Time to process: 16.97 seconds INFO 2025-10-20 23:25:40,596 process.py calibrate():227 [1] Calibration steps for 2019.311.00 INFO 2025-10-20 23:26:47,919 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 2025-10-20 23:26:47,921 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-10-20 23:26:50,397 calibrate.py _nudge_pos():1806 [1] 269: 0.150 -0.0078826 -0.0076087 59621 198.86 -5.891 -7.090 2019-11-07T20:45:31.183337472 INFO 2025-10-20 23:26:51,071 calibrate.py _nudge_pos():1806 [1] 332: 0.120 -0.0022843 0.0003671 6705 22.35 -15.189 3.044 2019-11-07T21:08:54.377212160 INFO 2025-10-20 23:26:51,775 calibrate.py _nudge_pos():1806 [1] 398: 0.170 -0.0006116 0.0002128 3970 13.23 -6.868 2.980 2019-11-07T21:23:13.378366464 INFO 2025-10-20 23:26:53,053 calibrate.py _nudge_pos():1806 [1] 513: 0.200 -0.0095737 -0.0094090 92465 308.40 -4.613 -5.653 2019-11-08T02:33:31.342559488 INFO 2025-10-20 23:26:56,206 calibrate.py _nudge_pos():1806 [1] 800: 0.050 -0.0017259 -0.0010955 6920 23.09 -11.105 -8.790 2019-11-08T03:01:23.345515008 INFO 2025-10-20 23:26:56,404 calibrate.py _nudge_pos():1806 [1] 818: 0.130 -0.0004404 0.0000947 44 0.14 -456.592 122.429 2019-11-08T03:01:49.143747840 INFO 2025-10-20 23:26:56,416 calibrate.py _nudge_pos():1806 [1] 819: 0.070 -0.0008186 -0.0018793 7922 26.40 -4.607 -13.189 2019-11-08T03:28:13.545208832 INFO 2025-10-20 23:26:57,442 calibrate.py _nudge_pos():1806 [1] 912: 0.180 -0.0012173 -0.0013285 6865 22.91 -7.895 -10.745 2019-11-08T03:52:40.349005312 INFO 2025-10-20 23:26:58,142 calibrate.py _nudge_pos():1806 [1] 976: 0.090 -0.0005589 -0.0052871 14075 46.95 -1.769 -20.868 2019-11-08T04:40:40.346058240 INFO 2025-10-20 23:26:58,856 calibrate.py _nudge_pos():1806 [1] 1041: 0.100 0.0009221 -0.0042983 14310 47.73 2.871 -16.687 2019-11-08T05:29:28.341468672 INFO 2025-10-20 23:26:59,648 calibrate.py _nudge_pos():1806 [1] 1113: 0.170 -0.0001219 -0.0001000 355 1.18 -15.357 -15.698 2019-11-08T05:31:50.341740800 INFO 2025-10-20 23:27:01,631 calibrate.py _nudge_pos():1806 [1] 1291: 0.190 0.0000157 -0.0055253 14155 47.21 0.049 -21.687 2019-11-08T06:22:00.350574080 INFO 2025-10-20 23:27:02,519 calibrate.py _nudge_pos():1806 [1] 1371: 0.140 -0.0001483 -0.0001790 334 1.11 -19.855 -29.887 2019-11-08T06:24:26.350572288 INFO 2025-10-20 23:27:03,287 calibrate.py _nudge_pos():1806 [1] 1439: 0.200 0.0001907 -0.0022085 5404 18.04 1.571 -22.685 2019-11-08T06:43:36.158822656 INFO 2025-10-20 23:27:23,630 calibrate.py _nudge_pos():1806 [1] 3218: 0.030 -0.0011249 -0.0015262 6940 23.13 -7.229 -12.226 2019-11-08T07:36:24.359953408 INFO 2025-10-20 23:27:24,401 calibrate.py _nudge_pos():1806 [1] 3285: 0.130 -0.0008288 -0.0010574 6835 22.78 -5.408 -8.602 2019-11-08T08:00:17.361786112 INFO 2025-10-20 23:27:26,747 calibrate.py _nudge_pos():1806 [1] 3491: 0.050 -0.0025787 -0.0011608 14331 47.80 -8.020 -4.500 2019-11-08T08:51:30.565755648 INFO 2025-10-20 23:27:45,457 calibrate.py _nudge_pos():1806 [1] 5127: 0.060 -0.0010295 -0.0004395 7261 24.20 -6.323 -3.366 2019-11-08T09:42:57.322478848 INFO 2025-10-20 23:27:54,631 calibrate.py _nudge_pos():1806 [1] 5880: 0.080 -0.0239267 -0.0166613 111927 373.31 -9.529 -8.270 2019-11-08T16:08:48.344828416 INFO 2025-10-20 23:27:55,495 calibrate.py _nudge_pos():1806 [1] 5953: 0.170 -0.0002518 -0.0004048 6885 22.95 -1.631 -3.269 2019-11-08T16:32:57.345565184 INFO 2025-10-20 23:27:57,339 calibrate.py _nudge_pos():1806 [1] 6109: 0.090 0.0000974 -0.0008531 6800 22.69 0.638 -6.966 2019-11-08T16:58:14.339630848 INFO 2025-10-20 23:28:00,614 calibrate.py _nudge_pos():1862 [1] 6335: - - - 2 0.00 - - INFO 2025-10-20 23:28:00,615 calibrate.py _nudge_pos():1868 [1] Points in final series = 425422 INFO 2025-10-20 23:28:18,122 calibrate.py _read_oxy_coeffs():1189 [1] Looking for calibration file for O2 sensor serial number 2935 on port side INFO 2025-10-20 23:28:18,123 calibrate.py _read_oxy_coeffs():1219 [1] Executing: find "/Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files" -name "2935" INFO 2025-10-20 23:28:18,346 calibrate.py _read_oxy_coeffs():1238 [1] Found calibration date dirs: 2014_Nov 2021_Mar 2022_Apr WARNING 2025-10-20 23:28:18,351 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2014_Nov INFO 2025-10-20 23:28:18,351 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:28:18,355 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2021_Mar INFO 2025-10-20 23:28:18,355 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:28:18,360 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr INFO 2025-10-20 23:28:18,360 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} INFO 2025-10-20 23:28:18,366 calibrate.py _read_oxy_coeffs():1247 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml has CalibrationDate 2022-03-22 00:00:00+00:00 INFO 2025-10-20 23:28:18,366 calibrate.py _read_oxy_coeffs():1253 [1] Breaking from loop as /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml is after 2019.311.00 with mission_start=2019-11-07T17:22:28.497233664 INFO 2025-10-20 23:28:18,366 calibrate.py _read_oxy_coeffs():1270 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml is the first calibration file, but is after 2019.311.00 with mission_start=2019-11-07T17:22:28.497233664 INFO 2025-10-20 23:28:19,100 calibrate.py _calibrated_oxygen():2513 [1] dissolvedO2_port: parsed from /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml file: {'Soc': 0.42595, 'offset': -0.5339, 'A': -0.0041113, 'B': 0.00020802, 'C': -3.0027e-06, 'D0': 2.5826, 'D1': 0.000192634, 'D2': -0.0464803, 'E': 0.036, 'Tau20': 1.09, 'H1': -0.033, 'H2': 5000.0, 'H3': 1450.0} INFO 2025-10-20 23:28:19,104 calibrate.py _read_oxy_coeffs():1189 [1] Looking for calibration file for O2 sensor serial number 3488 on stbd side INFO 2025-10-20 23:28:19,105 calibrate.py _read_oxy_coeffs():1219 [1] Executing: find "/Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files" -name "3488" INFO 2025-10-20 23:28:19,293 calibrate.py _read_oxy_coeffs():1238 [1] Found calibration date dirs: 2016_dec 2021_mar 2022_Jan WARNING 2025-10-20 23:28:19,298 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec INFO 2025-10-20 23:28:19,298 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:28:19,302 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2021_mar INFO 2025-10-20 23:28:19,302 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} WARNING 2025-10-20 23:28:19,306 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2022_Jan INFO 2025-10-20 23:28:19,306 calibrate.py _cal_date_xml_files():1087 [1] {xml_files} INFO 2025-10-20 23:28:19,312 calibrate.py _read_oxy_coeffs():1247 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml has CalibrationDate 2016-12-16 00:00:00+00:00 INFO 2025-10-20 23:28:19,312 calibrate.py _read_oxy_coeffs():1263 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml is just before 2019.311.00 with mission_start=2019-11-07T17:22:28.497233664 INFO 2025-10-20 23:28:20,047 calibrate.py _calibrated_oxygen():2513 [1] dissolvedO2_stbd: parsed from /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml file: {'Soc': 0.44664, 'offset': -0.507, 'A': -0.0030812, 'B': 7.8442e-05, 'C': -9.0601e-07, 'D0': 2.5826, 'D1': 0.000192634, 'D2': -0.0464803, 'E': 0.036, 'Tau20': 1.44, 'H1': -0.033, 'H2': 5000.0, 'H3': 1450.0} INFO 2025-10-20 23:28:21,068 calibrate.py _geometric_depth_correction():3423 [1] seabird25p: d_beg_time_diff: 2 seconds, d_end_time_diff: -80513 seconds INFO 2025-10-20 23:28:21,431 calibrate.py _geometric_depth_correction():3423 [1] seabird25p: d_beg_time_diff: 2 seconds, d_end_time_diff: -80513 seconds INFO 2025-10-20 23:28:21,433 calibrate.py _ctd_process():2919 [1] Performing range checking of ['seabird25p_salinity'] in 2019.311.00/seabird25p.nc WARNING 2025-10-20 23:28:21,434 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (1697) seabird25p_salinity values found outside of range. This may indicate a problem with the seabird25p data. INFO 2025-10-20 23:28:21,435 calibrate.py _range_qc_combined_nc():898 [1] Setting 1697 seabird25p_salinity values to NaN INFO 2025-10-20 23:28:21,435 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('seabird25p_salinity', Range(min=30, max=40))] INFO 2025-10-20 23:28:21,435 calibrate.py _range_qc_combined_nc():936 [1] Done range checking seabird25p INFO 2025-10-20 23:28:29,301 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_cal.nc INFO 2025-10-20 23:28:32,048 calibrate.py write_netcdf():3512 [1] Data variables written: depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_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, seabird25p_beam_transmittance, seabird25p_conductivity, seabird25p_conductivity_onboard, seabird25p_depth, seabird25p_dissolvedO2_port, seabird25p_dissolvedO2_stbd, seabird25p_oxygen_mll_port, seabird25p_oxygen_mll_stbd, seabird25p_oxygen_umolkg_port, seabird25p_oxygen_umolkg_stbd, seabird25p_salinity, seabird25p_salinity_onboard, seabird25p_temperature, seabird25p_temperature_onboard, seabird25p_time, tailcone_propRpm, tailcone_time, time INFO 2025-10-20 23:28:32,054 process.py align():251 [1] Alignment steps for 2019.311.00 INFO 2025-10-20 23:28:32,088 align.py process_cal():139 [1] Processing i2map_2019.311.00_cal.nc from /data/auv_data/i2map/missionnetcdfs/2019.311.00 INFO 2025-10-20 23:28:32,196 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-10-20 23:28:32,206 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-10-20 23:28:32,466 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-10-20 23:28:32,480 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-10-20 23:28:32,788 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-10-20 23:28:32,802 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-10-20 23:28:32,958 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-10-20 23:28:32,958 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-10-20 23:28:33,071 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-10-20 23:28:33,085 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-10-20 23:28:33,316 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,322 align.py process_cal():249 [1] seabird25p_temperature: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:33,415 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,418 align.py process_cal():249 [1] seabird25p_conductivity: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:33,511 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,515 align.py process_cal():249 [1] seabird25p_salinity: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:33,607 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,610 align.py process_cal():249 [1] seabird25p_temperature_onboard: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:33,706 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,710 align.py process_cal():249 [1] seabird25p_conductivity_onboard: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:33,802 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,805 align.py process_cal():249 [1] seabird25p_salinity_onboard: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:33,899 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,902 align.py process_cal():249 [1] seabird25p_dissolvedO2_port: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:33,995 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:33,998 align.py process_cal():249 [1] seabird25p_oxygen_mll_port: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:34,096 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:34,099 align.py process_cal():249 [1] seabird25p_oxygen_umolkg_port: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:34,207 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:34,211 align.py process_cal():249 [1] seabird25p_dissolvedO2_stbd: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:34,304 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:34,309 align.py process_cal():249 [1] seabird25p_oxygen_mll_stbd: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:34,399 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:34,402 align.py process_cal():249 [1] seabird25p_oxygen_umolkg_stbd: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:34,495 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:34,498 align.py process_cal():249 [1] seabird25p_beam_transmittance: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:34,589 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2019.311.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0) INFO 2025-10-20 23:28:34,591 align.py process_cal():249 [1] seabird25p_depth: instrument_sample_rate_hz = 7.99 INFO 2025-10-20 23:28:34,763 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-10-20 23:28:34,931 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_align.nc INFO 2025-10-20 23:28:35,012 align.py write_netcdf():342 [1] Data variables written: navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, seabird25p_beam_transmittance, seabird25p_conductivity, seabird25p_conductivity_onboard, seabird25p_depth, seabird25p_dissolvedO2_port, seabird25p_dissolvedO2_stbd, seabird25p_latitude, seabird25p_longitude, seabird25p_oxygen_mll_port, seabird25p_oxygen_mll_stbd, seabird25p_oxygen_umolkg_port, seabird25p_oxygen_umolkg_stbd, seabird25p_salinity, seabird25p_salinity_onboard, seabird25p_temperature, seabird25p_temperature_onboard, seabird25p_time, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-10-20 23:28:35,014 process.py resample():273 [1] Resampling steps for 2019.311.00 INFO 2025-10-20 23:28:35,014 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-10-20 23:28:35,035 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_align.nc mission netCDF file INFO 2025-10-20 23:28:35,041 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_align.nc mission netCDF file INFO 2025-10-20 23:28:35,044 resample.py get_mission_start_end():1145 [1] navigation: 2019-11-07T17:22:50.595719936 to 2019-11-08T17:02:41.741312512 (0 days 00:00:00 before mission_end) INFO 2025-10-20 23:28:35,047 resample.py get_mission_start_end():1145 [1] seabird25p: 2019-11-07T17:22:28.497233664 to 2019-11-07T18:40:49.541045504 (0 days 22:21:52.200267008 before mission_end) WARNING 2025-10-20 23:28:35,047 resample.py get_mission_start_end():1156 [1] Instrument seabird25p has a gap > 5 minutes at the end of the mission: 0 days 22:21:52.200267008 INFO 2025-10-20 23:28:35,051 resample.py get_mission_start_end():1145 [1] tailcone : 2019-11-07T17:22:16.228073984 to 2019-11-08T17:02:09.173543424 (0 days 00:00:32.567769088 before mission_end) INFO 2025-10-20 23:28:35,052 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_align.nc mission netCDF file INFO 2025-10-20 23:28:35,052 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:35,939 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,058 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,181 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,299 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,333 resample.py resample_variable():1031 [1] Resampling seabird25p_temperature with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,333 resample.py resample_variable():1038 [1] Padding seabird25p_temperature with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,359 resample.py resample_variable():1031 [1] Resampling seabird25p_conductivity with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,359 resample.py resample_variable():1038 [1] Padding seabird25p_conductivity with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,385 resample.py resample_variable():1031 [1] Resampling seabird25p_salinity with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,385 resample.py resample_variable():1038 [1] Padding seabird25p_salinity with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,407 resample.py resample_variable():1031 [1] Resampling seabird25p_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,408 resample.py resample_variable():1038 [1] Padding seabird25p_temperature_onboard with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,430 resample.py resample_variable():1031 [1] Resampling seabird25p_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,430 resample.py resample_variable():1038 [1] Padding seabird25p_conductivity_onboard with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,453 resample.py resample_variable():1031 [1] Resampling seabird25p_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,453 resample.py resample_variable():1038 [1] Padding seabird25p_salinity_onboard with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,475 resample.py resample_variable():1031 [1] Resampling seabird25p_dissolvedO2_port with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,476 resample.py resample_variable():1038 [1] Padding seabird25p_dissolvedO2_port with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,497 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_mll_port with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,498 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_mll_port with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,519 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_umolkg_port with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,520 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_umolkg_port with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,541 resample.py resample_variable():1031 [1] Resampling seabird25p_dissolvedO2_stbd with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,541 resample.py resample_variable():1038 [1] Padding seabird25p_dissolvedO2_stbd with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,563 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_mll_stbd with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,563 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_mll_stbd with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,586 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_umolkg_stbd with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,586 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_umolkg_stbd with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,608 resample.py resample_variable():1031 [1] Resampling seabird25p_beam_transmittance with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:36,608 resample.py resample_variable():1038 [1] Padding seabird25p_beam_transmittance with 0 days 22:21:52.200267008 of NaNs to the end of mission INFO 2025-10-20 23:28:36,725 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-10-20 23:28:37,246 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_1S.nc INFO 2025-10-20 23:28:37,247 process.py archive():337 [1] Archiving steps for 2019.311.00 INFO 2025-10-20 23:28:37,248 process.py archive():347 [1] nc_file_base = /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00, BASE_PATH = /data/auv_data INFO 2025-10-20 23:28:37,249 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00 files to /Volumes/AUVCTD/surveys/2019/netcdf INFO 2025-10-20 23:28:37,250 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2019/netcdf/i2map_2019.311.00_1S.nc INFO 2025-10-20 23:28:37,290 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_1S.nc /Volumes/AUVCTD/surveys/2019/netcdf done. INFO 2025-10-20 23:28:37,291 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2019/netcdf/i2map_2019.311.00_cal.nc INFO 2025-10-20 23:28:37,721 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_cal.nc /Volumes/AUVCTD/surveys/2019/netcdf done. INFO 2025-10-20 23:28:37,722 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2019/netcdf/i2map_2019.311.00_align.nc INFO 2025-10-20 23:28:37,846 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_align.nc /Volumes/AUVCTD/surveys/2019/netcdf done. INFO 2025-10-20 23:28:37,857 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019311/2019.311.00 done. INFO 2025-10-20 23:28:38,303 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019311/2019.311.00 done. INFO 2025-10-20 23:28:38,436 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019311/2019.311.00 done. INFO 2025-10-20 23:28:38,456 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/seabird25p.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019311/2019.311.00 done. INFO 2025-10-20 23:28:38,545 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2019/2019311/2019.311.00 done. INFO 2025-10-20 23:28:38,546 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-10-20 23:28:38,546 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2019.311.00/i2map_2019.311.00_processing.log /Volumes/AUVCTD/surveys/2019/netcdf