INFO 2025-06-26 13:33:32,016 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 13:33:32,016 process.py process_mission():434 [1] dorado_info[mission]["comment"] = OCCO mission - Northern shelf survey about ESP deployments - ctdToUse = ctd1 INFO 2025-06-26 13:33:32,016 process.py process_mission():449 [1] Processing OCCO mission 2007.263.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:33:32,016 process.py download_process():165 [1] Download and processing steps for 2007.263.01 INFO 2025-06-26 13:33:32,017 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007263/2007.263.01 INFO 2025-06-26 13:33:32,017 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007263/2007.263.01 to /data/auv_data/dorado/missionlogs/2007.263.01 INFO 2025-06-26 13:33:38,152 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.263.01 INFO 2025-06-26 13:33:38,152 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/ctdDriver.log (23568115 bytes) INFO 2025-06-26 13:33:39,874 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.263.01/ctdDriver.log: [ 195 560 845 881 1060 1366 1404 1419 1694 1825 1836 2232 3295 3506 4002 4985 5201 5232 6155 6165 7062 8203 9330 9391 9854 10220 10274 10674 11746 11941 13202 15310 16281 17404 17559 18736 19448 20091 20738 24157 25570 25604 26632 26883 29085 30836 32498 37553 38218 40015 43291 43687 44272 45481 48403 49093 49477 50963 52257 54277 56088 56089 60977 63838 64409 64471 66264 66813 70174 71117 71965 75556 81023 81696 86293 86951 87661 88134 91251 94455 95223 95248 96448 98013 102358 104677 106413 106814 111391 111505 116579 122586 124815 124874 125750 126629 130803 138248 150051 154441 155680 156894 157805 159249 161943 165090 166357 176940 178521 180578 183008 184197 185231 187691 191934 195851 198658 201391 201909 206934 209023 210345 212085 215749 216135 217283 218255 221932 230682 232220 242550 245647 246729 251693 251920 252365 254503 254590 255369 255489 258808 259080 259423 265792] INFO 2025-06-26 13:33:39,948 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/ctdDriver2.log (23579109 bytes) INFO 2025-06-26 13:33:41,664 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.263.01/ctdDriver2.log: [ 313 678 787 869 965 1002 1181 1539 1737 1813 1944 1955 2349 2732 3412 3624 4121 5107 5324 5355 6096 6287 7230 8323 9071 9450 9512 9975 10339 10394 10792 11864 12059 13321 13541 15433 16405 17531 17687 19578 20221 20868 22426 24289 25703 25737 27017 27092 29221 30320 30971 33881 37687 38351 43420 44400 45404 45607 45998 48528 49218 49601 56215 61109 64602 66945 70312 71254 72103 81166 81839 86437 87096 88280 90406 91360 91395 91778 93071 94209 95385 96585 96841 98150 102499 104818 106553 106954 116715 117077 122712 123466 124939 124997 125874 126753 135476 136642 138364 140715 146319 150170 154560 155800 157014 157925 158502 159370 162062 165212 166479 167245 176929 177060 178642 180703 184317 185352 187810 188378 192054 195972 198779 201515 202033 202930 203575 207058 209148 212206 212212 216251 217403 218374 222048 232330 242666 245645 245763 246845 251809 252036 252481 254707 255606 256845 258927 259199 259542 265913 267027] INFO 2025-06-26 13:33:41,749 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/gps.log (351356 bytes) INFO 2025-06-26 13:33:41,795 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/hydroscatlog.log (16100594 bytes) INFO 2025-06-26 13:33:43,672 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.263.01/hydroscatlog.log: [ 9 43 99 110 216 303 313 314 412 488 529 553 648 649 783 824 892 917 977 1074 1075 1112 1129 1294 1383 1602 1639 1656 1668 1730 1892 2067 2079 2235 2284 2285 2427 2476 2478 2479 2508 2820 2866 2892 3124 3280 3361 3454 3549 3670 3689 3762 3764 3765 4261 4262 4398 4399 4605 4881 5323 5376 5473 5474 5505 5655 6248 6429 6441 6752 7035 7339 7381 7756 8101 8133 8202 9236 10144 10511 10566 10738 10966 10986 11622 12043 12082 12240 12732 13503 13724 14556 15065 15195 15618 15879 16357 16592 17334 17721 17877 18419 19768 19769 20412 20413 20454 21872 22620 24459 24887 25698 25901 25936 26855 26965 26966 27218 27294 29422 30185 30525 30755 31178 31179 31372 32840 34090 34807 35972 37069 37328 37902 38715 40556 40613 42321 43640 44035 44622 45629 45630 45834 48756 49831 50548 51344 52952 56449 58060 58520 60066 61348 61445 64209 64210 64780 64781 64842 64843 66638 70555 71497 72281 74303 75947 76379 76798 78219 78470 78748 80984 81422 82097 84936 86698 86877 87968 88067 88541 88542 90669 91623 91658 92043 93343 93344 94483 94867 95658 95659 96860 97117 97118 98428 102369 102777 105095 106832 109868 116797 117003 117191 117371 118366 118532 120920 123016 123770 124879 126185 126764 127064 127065 131236 131962 132382 135716 135791 138353 138683 138684 139886 141037 142186 145395 147385 148291 148845 150497 152112 154888 156126 156574 157343 159626 159698 162394 165545 165889 166815 167580 169899 172264 176439 177138 177267 177401 178202 178983 178984 181045 183472 183473 184661 184662 185698 186950 187764 188158 188727 192403 192413 192849 195273 196323 198146 199132 199905 201867 203282 203928 205847 206298 207414 209504 210826 212091 212571 214916 216232 216618 217507 217770 218096 219283 223734 225998 226162 227406 229918 230629 230853 231179 232718 236096 237420 237965 238040 239433 244918 245081 245082 247043 247233 248591 252423 252868 252869 255008 255875 255995 257236 257985 259317 259318 259934 266304 266432 266433 267434] INFO 2025-06-26 13:33:43,726 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/navigation.log (78996878 bytes) INFO 2025-06-26 13:33:49,632 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/isuslog.log (1703029 bytes) INFO 2025-06-26 13:33:49,800 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/parosci.log (28188854 bytes) INFO 2025-06-26 13:33:52,240 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/tailCone.log (3289099 bytes) INFO 2025-06-26 13:33:52,651 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.263.01/biolume.log (18263580 bytes) INFO 2025-06-26 13:33:54,442 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:33:55,453 logs2netcdfs.py download_process_logs():807 [1] Time to process: 17.30 seconds WARNING 2025-06-26 13:33:55,453 process.py download_process():196 [1] No lopc.bin file for 2007.263.01 INFO 2025-06-26 13:33:55,453 process.py calibrate():227 [1] Calibration steps for 2007.263.01 INFO 2025-06-26 13:33:55,995 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 13:33:55,997 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:33:56,820 calibrate.py _nudge_pos():1806 [1] 103: 0.110 0.0000212 0.0001421 2288 7.85 0.400 3.355 2007-09-20T19:08:17.942011392 INFO 2025-06-26 13:33:57,698 calibrate.py _nudge_pos():1806 [1] 189: 0.110 0.0001494 -0.0002538 12642 42.48 0.521 -1.107 2007-09-20T19:52:11.941570048 INFO 2025-06-26 13:33:57,720 calibrate.py _nudge_pos():1806 [1] 191: 0.110 0.0000058 -0.0000024 120 0.40 2.154 -1.130 2007-09-20T19:52:36.939857408 INFO 2025-06-26 13:33:58,533 calibrate.py _nudge_pos():1806 [1] 268: 0.120 0.0001986 -0.0003653 14089 47.11 0.625 -1.437 2007-09-20T20:40:59.940988416 INFO 2025-06-26 13:33:59,415 calibrate.py _nudge_pos():1806 [1] 354: 0.120 0.0001591 -0.0002916 12505 41.80 0.564 -1.293 2007-09-20T21:24:12.943355648 INFO 2025-06-26 13:34:00,242 calibrate.py _nudge_pos():1806 [1] 434: 0.120 0.0002206 -0.0001176 13784 46.06 0.710 -0.473 2007-09-20T22:11:35.948596480 INFO 2025-06-26 13:34:00,285 calibrate.py _nudge_pos():1806 [1] 438: 0.120 0.0000299 -0.0000150 20 0.06 70.040 -43.973 2007-09-20T22:11:42.948116736 INFO 2025-06-26 13:34:01,118 calibrate.py _nudge_pos():1806 [1] 517: 0.130 0.0000172 -0.0000050 25 0.08 31.871 -11.606 2007-09-20T22:13:06.942362880 INFO 2025-06-26 13:34:01,139 calibrate.py _nudge_pos():1806 [1] 519: 0.130 0.0000009 -0.0001762 12510 41.76 0.003 -0.782 2007-09-20T22:54:53.940621568 INFO 2025-06-26 13:34:02,014 calibrate.py _nudge_pos():1806 [1] 601: 0.130 0.0001547 -0.0002176 10410 34.76 0.660 -1.160 2007-09-20T23:31:00.942172160 INFO 2025-06-26 13:34:02,749 calibrate.py _nudge_pos():1806 [1] 667: 0.140 0.0001631 -0.0001127 4015 13.40 1.806 -1.559 2007-09-20T23:45:29.942641152 INFO 2025-06-26 13:34:03,745 calibrate.py _nudge_pos():1806 [1] 752: 0.140 -0.0002376 -0.0001140 10781 36.00 -0.979 -0.587 2007-09-21T00:22:53.948916480 INFO 2025-06-26 13:34:04,428 calibrate.py _nudge_pos():1806 [1] 816: 0.140 -0.0001442 -0.0000901 6601 22.05 -0.969 -0.757 2007-09-21T00:45:59.943969280 INFO 2025-06-26 13:34:05,283 calibrate.py _nudge_pos():1806 [1] 894: 0.140 -0.0001206 -0.0000557 3813 12.71 -1.405 -0.811 2007-09-21T00:59:59.946425088 INFO 2025-06-26 13:34:06,096 calibrate.py _nudge_pos():1806 [1] 969: 0.150 -0.0000381 0.0003635 12800 42.76 -0.132 1.575 2007-09-21T01:43:59.945572864 INFO 2025-06-26 13:34:06,850 calibrate.py _nudge_pos():1806 [1] 1039: 0.160 -0.0000826 0.0003452 12268 40.95 -0.299 1.562 2007-09-21T02:26:05.942530048 INFO 2025-06-26 13:34:07,562 calibrate.py _nudge_pos():1806 [1] 1104: 0.160 -0.0001946 0.0005156 13434 44.83 -0.643 2.131 2007-09-21T03:11:59.943868160 INFO 2025-06-26 13:34:08,312 calibrate.py _nudge_pos():1806 [1] 1173: 0.170 -0.0001609 0.0003772 13622 45.46 -0.525 1.537 2007-09-21T03:58:35.942329088 INFO 2025-06-26 13:34:09,141 calibrate.py _nudge_pos():1806 [1] 1248: 0.180 -0.0000996 0.0006358 14186 47.36 -0.312 2.487 2007-09-21T04:47:11.942569472 INFO 2025-06-26 13:34:09,934 calibrate.py _nudge_pos():1806 [1] 1321: 0.170 0.0000557 0.0003312 5066 16.90 0.489 3.632 2007-09-21T05:05:17.948172800 INFO 2025-06-26 13:34:10,913 calibrate.py _nudge_pos():1806 [1] 1411: 0.180 0.0001459 0.0000674 10913 36.41 0.594 0.343 2007-09-21T05:43:11.942393600 INFO 2025-06-26 13:34:11,702 calibrate.py _nudge_pos():1806 [1] 1483: 0.190 0.0000883 0.0000259 5696 19.01 0.688 0.252 2007-09-21T06:03:23.939366144 INFO 2025-06-26 13:34:12,591 calibrate.py _nudge_pos():1806 [1] 1565: 0.190 0.0000493 -0.0000042 3105 10.35 0.706 -0.076 2007-09-21T06:15:05.941275904 INFO 2025-06-26 13:34:13,561 calibrate.py _nudge_pos():1806 [1] 1654: 0.190 0.0001749 -0.0003518 11545 38.53 0.672 -1.692 2007-09-21T06:55:05.946864128 INFO 2025-06-26 13:34:14,298 calibrate.py _nudge_pos():1806 [1] 1721: 0.190 0.0001129 -0.0001328 6887 22.99 0.727 -1.070 2007-09-21T07:19:11.947806208 INFO 2025-06-26 13:34:15,058 calibrate.py _nudge_pos():1806 [1] 1789: 0.200 0.0001056 -0.0001270 7367 24.58 0.636 -0.958 2007-09-21T07:44:53.942172416 INFO 2025-06-26 13:34:15,881 calibrate.py _nudge_pos():1806 [1] 1864: 0.200 0.0000726 -0.0001813 9547 31.86 0.337 -1.055 2007-09-21T08:17:59.946121728 INFO 2025-06-26 13:34:16,674 calibrate.py _nudge_pos():1806 [1] 1935: 0.200 0.0002168 -0.0002257 12084 40.33 0.796 -1.037 2007-09-21T08:59:29.945545216 INFO 2025-06-26 13:34:17,508 calibrate.py _nudge_pos():1806 [1] 2010: 0.010 0.0000773 0.0000183 3404 11.36 1.007 0.298 2007-09-21T09:12:06.143742208 INFO 2025-06-26 13:34:18,533 calibrate.py _nudge_pos():1806 [1] 2102: 0.010 0.0017709 0.0023318 13387 44.68 5.873 9.670 2007-09-21T09:58:18.143846912 INFO 2025-06-26 13:34:19,377 calibrate.py _nudge_pos():1806 [1] 2177: 0.020 0.0023515 0.0024194 12835 42.86 8.130 10.459 2007-09-21T10:42:24.142583552 INFO 2025-06-26 13:34:20,213 calibrate.py _nudge_pos():1806 [1] 2251: 0.020 0.0024387 0.0023240 12222 40.78 8.865 10.560 2007-09-21T11:24:24.139951872 INFO 2025-06-26 13:34:20,237 calibrate.py _nudge_pos():1806 [1] 2253: 0.020 -0.0000653 0.0001598 154 0.51 -18.855 57.662 2007-09-21T11:24:56.147759360 INFO 2025-06-26 13:34:21,113 calibrate.py _nudge_pos():1806 [1] 2331: 0.030 0.0024491 0.0023997 12335 41.18 8.818 10.798 2007-09-21T12:07:24.143209728 INFO 2025-06-26 13:34:21,942 calibrate.py _nudge_pos():1806 [1] 2402: 0.040 0.0021126 0.0020070 10094 33.70 9.298 11.036 2007-09-21T12:42:16.139898112 INFO 2025-06-26 13:34:22,743 calibrate.py _nudge_pos():1806 [1] 2473: 0.030 0.0009914 0.0005407 3671 12.26 11.990 8.170 2007-09-21T12:55:42.144683008 INFO 2025-06-26 13:34:23,521 calibrate.py _nudge_pos():1806 [1] 2542: 0.030 0.0000580 -0.0000065 440 1.46 5.879 -0.825 2007-09-21T12:58:18.143996160 INFO 2025-06-26 13:34:23,533 calibrate.py _nudge_pos():1806 [1] 2543: 0.030 0.0000184 -0.0000140 135 0.45 6.111 -5.795 2007-09-21T12:58:45.142146816 INFO 2025-06-26 13:34:50,022 calibrate.py _nudge_pos():1862 [1] 4837: - - - 0 0.00 - - INFO 2025-06-26 13:34:50,022 calibrate.py _nudge_pos():1868 [1] Points in final series = 334550 WARNING 2025-06-26 13:34:50,471 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 13:35:25,953 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:35:45,051 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 57 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:35:47,139 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 57 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:35:47,144 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.263.01/ctd1.nc INFO 2025-06-26 13:35:47,146 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:35:47,146 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 13:35:47,147 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:36:01,877 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:36:03,864 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:36:03,869 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.263.01/ctd2.nc INFO 2025-06-26 13:36:03,871 calibrate.py _range_qc_combined_nc():898 [1] Setting 134 ctd2_salinity values to NaN INFO 2025-06-26 13:36:03,871 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 13:36:03,871 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:36:03,968 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:36:07,086 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4014727 4014728 4014729] INFO 2025-06-26 13:36:07,729 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -6 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:36:07,737 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 13:36:07,741 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.263.01 ERROR 2025-06-26 13:36:07,741 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.263.01 INFO 2025-06-26 13:36:07,796 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_cal.nc INFO 2025-06-26 13:36:28,937 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 13:36:28,947 process.py align():251 [1] Alignment steps for 2007.263.01 INFO 2025-06-26 13:36:29,004 align.py process_cal():139 [1] Processing dorado_2007.263.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.263.01 INFO 2025-06-26 13:36:29,107 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:36:29,116 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:36:29,326 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:36:29,338 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:36:29,544 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:36:29,556 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:36:29,686 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:36:29,686 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:36:29,769 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:36:29,781 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:36:29,986 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:29,996 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:30,176 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:30,186 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:30,369 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:30,379 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:30,559 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:30,569 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:30,753 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:30,764 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:30,943 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:30,954 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:31,138 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:31,148 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:31,328 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:31,338 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:31,520 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:31,530 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:31,711 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:31,721 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:31,906 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:31,916 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:32,101 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:32,111 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:32,292 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:32,301 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:32,482 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:32,492 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:32,674 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:32,684 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:32,864 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:32,877 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:33,059 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:33,070 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:33,252 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:33,263 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:33,449 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:33,459 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:33,638 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.263.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:36:33,647 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:36:33,864 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 13:36:33,999 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 13:36:34,139 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 13:36:34,283 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:36:34,430 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 13:36:34,470 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_align.nc INFO 2025-06-26 13:36:34,616 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 13:36:34,618 process.py resample():273 [1] Resampling steps for 2007.263.01 INFO 2025-06-26 13:36:34,619 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:36:34,652 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_align.nc mission netCDF file INFO 2025-06-26 13:36:34,661 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_align.nc mission netCDF file INFO 2025-06-26 13:36:34,663 resample.py get_mission_start_end():1145 [1] navigation: 2007-09-20T18:59:17.109061120 to 2007-09-21T13:37:29.142941952 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 13:36:34,665 resample.py get_mission_start_end():1145 [1] hs2 : 2007-09-20T18:58:53.230696704 to 2007-09-21T13:37:29.102944512 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 13:36:34,668 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-09-20T18:59:45.927086848 to 2007-09-21T13:37:29.292931584 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:36:34,670 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-09-20T18:59:14.779220480 to 2007-09-21T13:37:29.282932224 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 13:36:34,672 resample.py get_mission_start_end():1145 [1] isus : 2007-09-20T19:00:03.455886080 to 2007-09-21T13:37:28.642976000 (0 days 00:00:00.649955584 before mission_end) INFO 2025-06-26 13:36:34,674 resample.py get_mission_start_end():1145 [1] biolume : 2007-09-20T18:58:42.211417344 to 2007-09-21T13:37:28.312964352 (0 days 00:00:00.979967232 before mission_end) INFO 2025-06-26 13:36:34,675 resample.py get_mission_start_end():1145 [1] tailcone : 2007-09-20T18:58:51.470817280 to 2007-09-21T13:37:28.832963072 (0 days 00:00:00.459968512 before mission_end) INFO 2025-06-26 13:36:34,676 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_align.nc mission netCDF file INFO 2025-06-26 13:36:34,676 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:35,364 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:35,472 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:35,578 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:35,686 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:35,777 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:35,868 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:35,958 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,047 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,131 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,213 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,296 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,380 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,463 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,547 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,630 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,712 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,799 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,891 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:36,984 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,072 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,160 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,248 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,282 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,313 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,342 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,376 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,409 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:36:37,876 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_1S.nc INFO 2025-06-26 13:36:40,606 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:36:51,586 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.263.01/dorado_2007.263.01_1S_Gulper.txt INFO 2025-06-26 13:36:51,586 process.py archive():337 [1] Archiving steps for 2007.263.01 INFO 2025-06-26 13:36:51,586 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01, BASE_PATH = /data/auv_data INFO 2025-06-26 13:36:51,588 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:36:51,588 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.263.01_1S.nc INFO 2025-06-26 13:36:51,636 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:36:51,637 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.263.01_cal.nc INFO 2025-06-26 13:36:51,866 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:36:51,867 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.263.01_align.nc INFO 2025-06-26 13:36:52,091 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:36:52,151 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,212 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,218 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,258 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,462 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,472 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,554 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,569 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,752 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007263/2007.263.01 done. INFO 2025-06-26 13:36:52,753 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:36:52,754 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.263.01_1S_Gulper.txt INFO 2025-06-26 13:36:52,759 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.263.01/dorado_2007.263.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 13:36:52,759 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.263.01/dorado_2007.263.01_processing.log /Volumes/AUVCTD/surveys/2007/netcdf