INFO 2025-06-26 13:18:30,131 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 13:18:30,131 process.py process_mission():434 [1] dorado_info[mission]["comment"] = OCCO mission - Canyon axis survey - ctdToUse = ctd1 INFO 2025-06-26 13:18:30,131 process.py process_mission():449 [1] Processing OCCO mission 2007.254.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:18:30,131 process.py download_process():165 [1] Download and processing steps for 2007.254.01 INFO 2025-06-26 13:18:30,131 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007254/2007.254.01 INFO 2025-06-26 13:18:30,132 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007254/2007.254.01 to /data/auv_data/dorado/missionlogs/2007.254.01 INFO 2025-06-26 13:18:36,725 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.254.01 INFO 2025-06-26 13:18:36,726 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/ctdDriver.log (25297315 bytes) INFO 2025-06-26 13:18:38,539 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.254.01/ctdDriver.log: [ 15 222 546 559 694 966 1158 1444 1489 1528 1536 1540 1749 2287 2343 2701 2723 3385 3535 3610 5148 5231 5325 6295 6541 7790 8014 8286 9538 10113 11249 11329 11454 12069 12500 13448 14836 16861 19276 20201 21713 23286 23681 27082 28315 30265 31490 32674 33542 37632 40616 41724 42100 42531 45372 45625 46330 48266 62172 65070 66962 73796 74078 78854 80487 87036 98650 102840 103431 104609 108539 109650 111249 120091 120340 124622 132118 133462 135433 135606 135875 136397 138106 138385 138946 140266 140554 141951 145222 149080 150772 152339 154634 159451 162133 166254 171974 173687 175503 183543 191543 199395 199641 200039 201733 202348 207146 208293 209261 218868 219960 222149 223491 226264 226721 227900 232320 235110 242524 256359 259647 262910 266175 270517 272610 273187 273291 278183 278860 279727 279991 282150 283715] INFO 2025-06-26 13:18:38,613 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/ctdDriver2.log (25298365 bytes) INFO 2025-06-26 13:18:40,459 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.254.01/ctdDriver2.log: [ 556 745 1154 1441 1523 1530 1534 1744 2089 2283 3344 3534 3608 5146 5324 6541 7981 8015 11333 11908 12076 12506 13454 14842 17714 18845 19283 19342 19581 20209 21723 23295 27093 27899 28326 30277 31502 32686 40623 41732 42002 42108 42539 45379 45631 46335 48270 51648 62179 65080 66972 68499 69197 73810 78868 80501 93555 95341 98669 99629 103451 104629 108559 109669 111270 120109 120358 125529 130339 132134 133478 135449 135622 138121 138963 140282 140571 141967 145238 150785 152352 154648 159466 162147 166267 166833 171984 173694 190654 191550 192147 199647 200046 201740 202356 202926 206122 207156 208302 209270 218876 219969 222132 222157 223499 226272 226729 227908 228989 232991 242534 252158 255589 256372 259660 259858 262923 266187 270530 272624 273201 273306 278199 279741 280005 282164 283729] INFO 2025-06-26 13:18:40,543 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/gps.log (136868 bytes) INFO 2025-06-26 13:18:40,567 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/hydroscatlog.log (17259314 bytes) INFO 2025-06-26 13:18:42,553 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.254.01/hydroscatlog.log: [ 3 13 36 65 78 81 84 85 216 293 305 307 461 533 726 773 804 830 835 877 878 939 1079 1107 1244 1409 1577 1579 1580 1617 1618 1626 1631 1639 2176 2188 2197 2334 2363 2387 2444 2803 3181 3280 3311 3446 3526 3643 3644 3658 3719 3720 4387 5116 5167 5168 5223 5262 5346 5460 6414 6659 6726 7770 7911 8103 8410 9553 9987 10241 11109 11378 11459 11584 11883 12035 12161 12203 12587 12635 13583 14261 14542 14971 15768 16999 17295 18194 18976 19415 19473 19474 19606 19712 20763 21330 21857 22463 23429 23824 24421 24921 27198 27234 28035 28463 28464 30416 31529 31539 31640 31928 33693 35853 35854 36289 38193 38659 40711 41876 42146 42253 42683 43413 45077 45526 46483 46484 48419 49275 49560 49763 51795 52891 56732 57257 58509 58698 60004 60706 60873 62327 64546 64761 64838 65226 68374 68645 68963 69344 71649 71943 72271 73955 73956 74239 78657 79011 79216 79769 80703 81355 82168 85378 87195 87271 88369 88469 89511 92096 93699 94773 95486 96014 98814 100577 102698 102825 103006 103598 105533 108705 109817 110010 111416 112250 116926 117284 118961 119320 120257 120506 123310 124041 124788 125679 130487 131151 133627 135596 135770 138270 138271 138551 139793 140688 140721 142119 143154 145389 145831 147300 149245 150935 152503 152546 159256 159614 159869 160348 162299 165973 165974 166418 166728 166984 169797 172693 173503 173850 175919 177303 179411 180965 183702 183703 184801 190807 191703 191704 192841 195187 197241 197420 197421 199553 199800 200199 201893 202304 202305 202510 203733 206276 207309 208456 209425 212086 212993 214641 214810 216536 219029 219707 222313 223653 226427 229813 230767 235271 237885 238477 240053 242688 243408 246578 246579 252115 252117 252119 252121 252891 255206 255753 259237 259824 259825 260023 263088 263251 266354 266738 270694 272788 273453 273470 274827 278361 279037 279903 280167 282329 282455 283298 286153 286280 286885 287363] INFO 2025-06-26 13:18:42,608 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/navigation.log (84714214 bytes) INFO 2025-06-26 13:18:48,829 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/isuslog.log (0 bytes) WARNING 2025-06-26 13:18:48,829 logs2netcdfs.py download_process_logs():790 [1] /data/auv_data/dorado/missionlogs/2007.254.01/isuslog.log is empty INFO 2025-06-26 13:18:48,830 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/parosci.log (30251366 bytes) INFO 2025-06-26 13:18:51,363 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/tailCone.log (3485995 bytes) INFO 2025-06-26 13:18:51,804 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.254.01/biolume.log (19578972 bytes) INFO 2025-06-26 13:18:53,674 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:18:54,695 logs2netcdfs.py download_process_logs():807 [1] Time to process: 17.97 seconds WARNING 2025-06-26 13:18:54,696 process.py download_process():196 [1] No lopc.bin file for 2007.254.01 INFO 2025-06-26 13:18:54,696 process.py calibrate():227 [1] Calibration steps for 2007.254.01 INFO 2025-06-26 13:18:55,301 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 13:18:55,304 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:18:56,098 calibrate.py _nudge_pos():1806 [1] 104: 0.050 -0.0001858 0.0000146 30 0.10 -285.444 27.954 2007-09-11T21:48:38.047882240 INFO 2025-06-26 13:18:56,209 calibrate.py _nudge_pos():1806 [1] 115: 0.060 0.0000163 0.0004248 3577 12.20 0.198 6.454 2007-09-11T22:01:00.047052032 INFO 2025-06-26 13:18:56,806 calibrate.py _nudge_pos():1806 [1] 174: 0.060 -0.0017225 0.0001673 16275 54.53 -4.690 0.568 2007-09-11T22:56:30.048931072 INFO 2025-06-26 13:18:57,390 calibrate.py _nudge_pos():1806 [1] 231: 0.070 -0.0003644 0.0011485 9769 32.66 -1.656 6.516 2007-09-11T23:30:06.050825472 INFO 2025-06-26 13:18:57,814 calibrate.py _nudge_pos():1806 [1] 272: 0.060 -0.0000482 -0.0000438 70 0.23 -31.112 -35.320 2007-09-11T23:31:00.047126528 INFO 2025-06-26 13:18:57,856 calibrate.py _nudge_pos():1806 [1] 276: 0.070 -0.0045185 0.0017117 16431 54.86 -12.230 5.781 2007-09-12T00:25:55.051403264 INFO 2025-06-26 13:18:58,307 calibrate.py _nudge_pos():1806 [1] 318: 0.070 -0.0000467 -0.0000059 15 0.05 -148.772 -23.284 2007-09-12T00:26:40.048321024 INFO 2025-06-26 13:18:58,418 calibrate.py _nudge_pos():1806 [1] 326: 0.070 -0.0000194 0.0000090 30 0.10 -29.750 17.164 2007-09-12T00:26:53.047430400 INFO 2025-06-26 13:18:58,475 calibrate.py _nudge_pos():1806 [1] 331: 0.070 -0.0041737 -0.0001789 8730 29.15 -21.267 -1.137 2007-09-12T00:56:06.047341568 INFO 2025-06-26 13:18:59,344 calibrate.py _nudge_pos():1806 [1] 412: 0.070 -0.0013826 -0.0002281 11496 38.36 -5.353 -1.102 2007-09-12T01:35:48.044163584 INFO 2025-06-26 13:19:00,206 calibrate.py _nudge_pos():1806 [1] 493: 0.070 -0.0042971 0.0038126 17241 57.55 -11.091 12.277 2007-09-12T02:34:42.052067584 INFO 2025-06-26 13:19:00,707 calibrate.py _nudge_pos():1806 [1] 539: 0.070 -0.0000817 0.0000051 20 0.06 -191.712 14.985 2007-09-12T02:35:31.048711168 INFO 2025-06-26 13:19:00,815 calibrate.py _nudge_pos():1806 [1] 549: 0.080 -0.0096213 -0.0011170 14454 48.26 -29.613 -4.289 2007-09-12T03:23:56.049704704 INFO 2025-06-26 13:19:01,631 calibrate.py _nudge_pos():1806 [1] 625: 0.080 -0.0101578 -0.0004912 14896 49.71 -30.355 -1.831 2007-09-12T04:14:54.050217472 INFO 2025-06-26 13:19:01,687 calibrate.py _nudge_pos():1806 [1] 630: 0.090 -0.0101743 -0.0004978 25 0.08 -18895.223 -1153.178 2007-09-12T04:15:03.049601024 INFO 2025-06-26 13:19:02,084 calibrate.py _nudge_pos():1806 [1] 665: 0.090 -0.0102778 -0.0004586 80 0.26 -5798.729 -322.724 2007-09-12T04:15:53.046176000 INFO 2025-06-26 13:19:02,883 calibrate.py _nudge_pos():1806 [1] 739: 0.090 -0.0084180 0.0032941 17223 57.50 -21.752 10.616 2007-09-12T05:14:36.044834048 INFO 2025-06-26 13:19:03,607 calibrate.py _nudge_pos():1806 [1] 806: 0.080 -0.0025773 0.0019770 5093 17.00 -22.529 21.554 2007-09-12T05:32:42.050437632 INFO 2025-06-26 13:19:04,417 calibrate.py _nudge_pos():1806 [1] 877: 0.090 -0.0016476 0.0008943 17779 59.33 -4.125 2.793 2007-09-12T06:33:12.051765504 INFO 2025-06-26 13:19:05,221 calibrate.py _nudge_pos():1806 [1] 950: 0.090 -0.0013209 0.0024332 17553 58.60 -3.349 7.695 2007-09-12T07:33:00.045970944 INFO 2025-06-26 13:19:05,990 calibrate.py _nudge_pos():1806 [1] 1019: 0.090 0.0013747 0.0035757 17549 58.56 3.487 11.314 2007-09-12T08:32:42.050586880 INFO 2025-06-26 13:19:06,763 calibrate.py _nudge_pos():1806 [1] 1089: 0.090 0.0021480 0.0043875 17724 59.15 5.394 13.745 2007-09-12T09:33:00.052736768 INFO 2025-06-26 13:19:07,560 calibrate.py _nudge_pos():1806 [1] 1158: 0.090 0.0014255 0.0019902 9123 30.46 6.950 12.106 2007-09-12T10:04:36.052851968 INFO 2025-06-26 13:19:08,306 calibrate.py _nudge_pos():1806 [1] 1216: 0.100 0.0035312 0.0030344 18324 61.15 8.576 9.195 2007-09-12T11:06:42.047603968 INFO 2025-06-26 13:19:09,003 calibrate.py _nudge_pos():1806 [1] 1279: 0.100 0.0012079 0.0008547 9164 30.56 5.869 5.182 2007-09-12T11:38:18.047718656 INFO 2025-06-26 13:19:09,764 calibrate.py _nudge_pos():1806 [1] 1348: 0.100 0.0015943 0.0009302 17749 59.26 3.994 2.908 2007-09-12T12:38:42.049457664 INFO 2025-06-26 13:19:09,947 calibrate.py _nudge_pos():1806 [1] 1364: 0.100 -0.0000345 -0.0000321 35 0.11 -45.148 -52.513 2007-09-12T12:39:04.047950848 INFO 2025-06-26 13:19:10,302 calibrate.py _nudge_pos():1806 [1] 1396: 0.100 0.0006842 -0.0001532 9171 30.61 3.318 -0.927 2007-09-12T13:10:12.049983744 INFO 2025-06-26 13:19:10,894 calibrate.py _nudge_pos():1806 [1] 1450: 0.110 0.0024618 -0.0016133 17648 58.91 6.203 -5.074 2007-09-12T14:10:00.044189440 INFO 2025-06-26 13:19:11,536 calibrate.py _nudge_pos():1806 [1] 1508: 0.110 0.0011199 -0.0006536 9121 30.45 5.460 -3.978 2007-09-12T14:41:24.045126400 INFO 2025-06-26 13:19:12,229 calibrate.py _nudge_pos():1806 [1] 1570: 0.110 0.0016207 -0.0008222 14099 47.08 5.110 -3.236 2007-09-12T15:29:30.047421696 INFO 2025-06-26 13:19:12,822 calibrate.py _nudge_pos():1806 [1] 1623: 0.100 0.0006639 -0.0004316 7404 24.73 3.985 -3.234 2007-09-12T15:55:06.052198144 INFO 2025-06-26 13:19:13,216 calibrate.py _nudge_pos():1806 [1] 1658: 0.110 -0.0000063 0.0000052 15 0.05 -20.047 20.679 2007-09-12T15:55:45.049526784 INFO 2025-06-26 13:19:13,405 calibrate.py _nudge_pos():1806 [1] 1675: 0.110 0.0015219 -0.0006073 12461 41.58 5.432 -2.707 2007-09-12T16:37:36.047511552 INFO 2025-06-26 13:19:13,973 calibrate.py _nudge_pos():1806 [1] 1725: 0.120 0.0006976 -0.0000259 6495 21.68 4.775 -0.222 2007-09-12T17:00:06.045030400 INFO 2025-06-26 13:19:14,550 calibrate.py _nudge_pos():1806 [1] 1776: 0.120 0.0020467 0.0000747 12993 43.36 7.003 0.319 2007-09-12T17:44:18.043356160 INFO 2025-06-26 13:19:15,815 calibrate.py _nudge_pos():1862 [1] 1855: - - - 5 0.01 - - INFO 2025-06-26 13:19:15,815 calibrate.py _nudge_pos():1868 [1] Points in final series = 358950 WARNING 2025-06-26 13:19:16,296 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 13:19:54,285 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:20:14,837 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:20:16,954 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:20:16,958 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.254.01/ctd1.nc INFO 2025-06-26 13:20:16,960 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:20:16,961 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 13:20:16,961 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:20:32,751 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:20:34,871 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:20:34,875 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.254.01/ctd2.nc INFO 2025-06-26 13:20:34,877 calibrate.py _range_qc_combined_nc():898 [1] Setting 155 ctd2_salinity values to NaN INFO 2025-06-26 13:20:34,877 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 13:20:34,877 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 13:20:34,877 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.254.01 INFO 2025-06-26 13:20:34,931 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:20:38,280 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4314148 4314149 4314150] INFO 2025-06-26 13:20:39,081 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -6 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:20:39,088 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 13:20:39,089 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.254.01 ERROR 2025-06-26 13:20:39,089 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.254.01 INFO 2025-06-26 13:20:39,149 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_cal.nc INFO 2025-06-26 13:21:01,528 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, 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 13:21:01,533 process.py align():251 [1] Alignment steps for 2007.254.01 INFO 2025-06-26 13:21:01,575 align.py process_cal():139 [1] Processing dorado_2007.254.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.254.01 INFO 2025-06-26 13:21:01,670 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:21:01,680 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:21:01,910 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:21:01,924 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:21:02,148 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:21:02,161 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:21:02,293 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:21:02,293 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:21:02,385 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:21:02,398 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:21:02,619 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:02,631 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:02,825 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:02,836 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:03,029 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:03,039 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:03,229 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:03,239 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:03,464 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:03,478 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:03,670 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:03,681 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:03,881 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:03,892 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:04,085 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:04,095 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:04,291 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:04,302 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:04,494 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:04,504 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:04,699 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:04,713 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:04,907 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:04,917 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:05,116 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:05,126 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:05,323 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:05,339 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:05,544 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:05,558 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:05,757 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:05,768 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:05,963 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:05,977 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:06,176 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:06,188 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:06,384 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:06,395 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:06,590 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.254.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:21:06,600 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:21:06,840 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:21:06,993 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 13:21:07,039 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_align.nc INFO 2025-06-26 13:21:07,184 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, 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 13:21:07,186 process.py resample():273 [1] Resampling steps for 2007.254.01 INFO 2025-06-26 13:21:07,187 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:21:07,218 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_align.nc mission netCDF file INFO 2025-06-26 13:21:07,227 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_align.nc mission netCDF file INFO 2025-06-26 13:21:07,229 resample.py get_mission_start_end():1145 [1] navigation: 2007-09-11T21:47:22.883031552 to 2007-09-12T17:46:11.045614848 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 13:21:07,232 resample.py get_mission_start_end():1145 [1] hs2 : 2007-09-11T21:47:03.274374912 to 2007-09-12T17:46:10.945621760 (0 days 00:00:00.209985792 before mission_end) INFO 2025-06-26 13:21:07,235 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-09-11T21:47:19.803242496 to 2007-09-12T17:46:11.155607552 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:21:07,237 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-09-11T21:47:20.383202816 to 2007-09-12T17:46:10.945621760 (0 days 00:00:00.209985792 before mission_end) INFO 2025-06-26 13:21:07,239 resample.py get_mission_start_end():1145 [1] biolume : 2007-09-11T21:46:48.425357824 to 2007-09-12T17:46:10.025650432 (0 days 00:00:01.129957120 before mission_end) INFO 2025-06-26 13:21:07,241 resample.py get_mission_start_end():1145 [1] tailcone : 2007-09-11T21:46:54.045007104 to 2007-09-12T17:46:10.515651328 (0 days 00:00:00.639956224 before mission_end) INFO 2025-06-26 13:21:07,241 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_align.nc mission netCDF file INFO 2025-06-26 13:21:07,242 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:07,997 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,121 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,235 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,349 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,448 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,545 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,641 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,736 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,826 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:08,916 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,008 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,099 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,189 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,278 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,368 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,459 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,554 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,647 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,747 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,839 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:09,930 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:10,023 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:10,062 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:10,100 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:21:10,610 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_1S.nc INFO 2025-06-26 13:21:14,085 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:21:17,917 create_products.py gulper_odv():522 [1] Wrote 4 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.254.01/dorado_2007.254.01_1S_Gulper.txt INFO 2025-06-26 13:21:17,917 process.py archive():337 [1] Archiving steps for 2007.254.01 INFO 2025-06-26 13:21:17,918 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01, BASE_PATH = /data/auv_data INFO 2025-06-26 13:21:17,919 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:21:17,920 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.254.01_1S.nc INFO 2025-06-26 13:21:17,968 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:21:17,969 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.254.01_cal.nc INFO 2025-06-26 13:21:18,222 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:21:18,223 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.254.01_align.nc INFO 2025-06-26 13:21:18,452 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:21:18,528 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:18,597 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:18,602 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:18,652 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:18,867 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:18,960 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:18,978 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:19,195 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007254/2007.254.01 done. INFO 2025-06-26 13:21:19,196 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:21:19,197 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.254.01_1S_Gulper.txt INFO 2025-06-26 13:21:19,202 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.254.01/dorado_2007.254.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 13:21:19,202 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.254.01/dorado_2007.254.01_processing.log /Volumes/AUVCTD/surveys/2007/netcdf