INFO 2025-06-26 11:18:19,248 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 11:18:19,248 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Unattended BIOLUME mission - C1 to M2 and back - a lot of data collecetd in the last 48 hours. (After strong wind event.) - ctdToUse = ctd1 INFO 2025-06-26 11:18:19,248 process.py process_mission():449 [1] Processing BIOLUME mission 2006.130.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:18:19,248 process.py download_process():165 [1] Download and processing steps for 2006.130.01 INFO 2025-06-26 11:18:19,248 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006130/2006.130.01 INFO 2025-06-26 11:18:19,248 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006130/2006.130.01 to /data/auv_data/dorado/missionlogs/2006.130.01 INFO 2025-06-26 11:18:25,894 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.130.01 INFO 2025-06-26 11:18:25,895 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/ctdDriver.log (23654355 bytes) INFO 2025-06-26 11:18:27,654 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/ctdDriver2.log (23654261 bytes) INFO 2025-06-26 11:18:29,438 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/gps.log (141836 bytes) INFO 2025-06-26 11:18:29,461 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/hydroscatlog.log (16125854 bytes) INFO 2025-06-26 11:18:31,348 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/navigation.log (79298014 bytes) INFO 2025-06-26 11:18:37,065 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/isuslog.log (1445397 bytes) INFO 2025-06-26 11:18:37,208 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/parosci.log (34556054 bytes) INFO 2025-06-26 11:18:39,989 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.130.01/parosci.log: [ 7440 7441 7442 7443 7444 657937 657938 657939] INFO 2025-06-26 11:18:40,083 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/tailCone.log (16133611 bytes) INFO 2025-06-26 11:18:42,037 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.130.01/biolume.log (18290236 bytes) INFO 2025-06-26 11:18:43,761 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:18:44,680 logs2netcdfs.py download_process_logs():807 [1] Time to process: 18.79 seconds WARNING 2025-06-26 11:18:44,681 process.py download_process():196 [1] No lopc.bin file for 2006.130.01 INFO 2025-06-26 11:18:44,681 process.py calibrate():227 [1] Calibration steps for 2006.130.01 INFO 2025-06-26 11:18:45,130 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 11:18:45,133 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:18:45,891 calibrate.py _nudge_pos():1806 [1] 90: 0.050 -0.0007488 -0.0009151 5889 19.63 -5.662 -8.638 2006-05-10T22:19:53.927591808 INFO 2025-06-26 11:18:45,913 calibrate.py _nudge_pos():1806 [1] 92: 0.030 0.0000268 -0.0000113 15 0.05 85.143 -44.725 2006-05-10T22:19:57.927317888 INFO 2025-06-26 11:18:46,536 calibrate.py _nudge_pos():1806 [1] 153: 0.050 0.0035432 0.0014304 11167 37.23 14.128 7.119 2006-05-10T22:58:11.930167936 INFO 2025-06-26 11:18:46,924 calibrate.py _nudge_pos():1806 [1] 191: 0.040 0.0000670 -0.0000588 30 0.10 102.858 -112.734 2006-05-10T22:58:54.927222272 INFO 2025-06-26 11:18:47,095 calibrate.py _nudge_pos():1806 [1] 207: 0.040 0.0002618 0.0037345 13747 45.83 0.848 15.099 2006-05-10T23:44:59.927806848 INFO 2025-06-26 11:18:47,929 calibrate.py _nudge_pos():1806 [1] 288: 0.050 -0.0035201 0.0008460 10130 33.76 -15.479 4.643 2006-05-11T00:20:05.923536256 INFO 2025-06-26 11:18:48,703 calibrate.py _nudge_pos():1806 [1] 364: 0.050 -0.0025026 0.0031036 10737 35.80 -10.381 16.066 2006-05-11T00:57:08.931249664 INFO 2025-06-26 11:18:48,808 calibrate.py _nudge_pos():1806 [1] 374: 0.050 0.0000066 0.0000158 35 0.11 8.662 25.873 2006-05-11T00:57:24.930153856 INFO 2025-06-26 11:18:49,147 calibrate.py _nudge_pos():1806 [1] 407: 0.070 -0.0025772 0.0025962 12375 41.25 -9.278 11.663 2006-05-11T01:39:11.928412672 INFO 2025-06-26 11:18:49,551 calibrate.py _nudge_pos():1806 [1] 445: 0.070 -0.0045300 0.0008653 9265 30.88 -21.786 5.192 2006-05-11T02:10:41.928938624 INFO 2025-06-26 11:18:50,052 calibrate.py _nudge_pos():1806 [1] 492: 0.070 -0.0017159 0.0043742 10095 33.65 -7.574 24.090 2006-05-11T02:45:06.927476608 INFO 2025-06-26 11:18:50,881 calibrate.py _nudge_pos():1806 [1] 572: 0.070 -0.0016892 0.0064180 14744 49.15 -5.105 24.198 2006-05-11T03:35:35.929975808 INFO 2025-06-26 11:18:51,328 calibrate.py _nudge_pos():1806 [1] 614: 0.080 -0.0000703 -0.0001511 20 0.06 -164.934 -442.033 2006-05-11T03:36:20.926893184 INFO 2025-06-26 11:18:51,404 calibrate.py _nudge_pos():1806 [1] 621: 0.080 0.0024848 0.0022572 13260 44.20 8.351 9.464 2006-05-11T04:20:41.924602240 INFO 2025-06-26 11:18:51,460 calibrate.py _nudge_pos():1806 [1] 626: 0.080 0.0000327 0.0000425 15 0.05 104.026 168.588 2006-05-11T04:20:49.924054400 INFO 2025-06-26 11:18:51,546 calibrate.py _nudge_pos():1806 [1] 634: 0.080 0.0000633 0.0000470 20 0.06 148.513 137.592 2006-05-11T04:21:01.923232256 INFO 2025-06-26 11:18:51,578 calibrate.py _nudge_pos():1806 [1] 637: 0.080 -0.0000172 -0.0000004 15 0.05 -54.504 -1.596 2006-05-11T04:21:06.932889216 INFO 2025-06-26 11:18:51,632 calibrate.py _nudge_pos():1806 [1] 642: 0.080 0.0000033 -0.0000168 20 0.06 7.677 -49.197 2006-05-11T04:21:14.932341120 INFO 2025-06-26 11:18:51,967 calibrate.py _nudge_pos():1806 [1] 673: 0.070 0.0000036 0.0000146 80 0.26 2.032 10.302 2006-05-11T04:22:01.929121792 INFO 2025-06-26 11:18:51,990 calibrate.py _nudge_pos():1806 [1] 675: 0.080 0.0011598 0.0026758 13545 45.15 3.816 10.983 2006-05-11T05:07:11.923474304 INFO 2025-06-26 11:18:52,025 calibrate.py _nudge_pos():1806 [1] 678: 0.090 -0.0000117 0.0000066 15 0.05 -37.238 26.315 2006-05-11T05:07:17.923063296 INFO 2025-06-26 11:18:52,431 calibrate.py _nudge_pos():1806 [1] 715: 0.090 -0.0000639 -0.0000473 105 0.35 -27.367 -25.274 2006-05-11T05:08:14.929158272 INFO 2025-06-26 11:18:52,495 calibrate.py _nudge_pos():1806 [1] 721: 0.110 -0.0033994 0.0062736 14860 49.53 -10.196 23.471 2006-05-11T05:57:53.925082880 INFO 2025-06-26 11:18:52,622 calibrate.py _nudge_pos():1806 [1] 733: 0.090 -0.0034606 0.0062817 60 0.20 -2614.231 5919.037 2006-05-11T05:58:16.923507456 INFO 2025-06-26 11:18:52,655 calibrate.py _nudge_pos():1806 [1] 736: 0.090 -0.0034135 0.0062966 25 0.08 -6339.164 14585.422 2006-05-11T05:58:23.923027968 INFO 2025-06-26 11:18:52,944 calibrate.py _nudge_pos():1806 [1] 763: 0.080 -0.0035083 0.0062970 75 0.25 -2113.034 4730.740 2006-05-11T05:59:04.930218752 INFO 2025-06-26 11:18:53,346 calibrate.py _nudge_pos():1806 [1] 800: 0.090 -0.0000816 0.0000037 45 0.15 -82.662 4.725 2006-05-11T05:59:49.927136128 INFO 2025-06-26 11:18:53,390 calibrate.py _nudge_pos():1806 [1] 804: 0.080 0.0000232 0.0000550 20 0.06 54.381 160.950 2006-05-11T05:59:57.926588288 INFO 2025-06-26 11:18:53,413 calibrate.py _nudge_pos():1806 [1] 806: 0.090 -0.0034335 0.0021460 5675 18.91 -26.972 21.025 2006-05-11T06:18:53.928766720 INFO 2025-06-26 11:18:54,016 calibrate.py _nudge_pos():1806 [1] 862: 0.090 0.0024083 0.0049814 15621 52.08 6.869 17.724 2006-05-11T07:11:53.930921856 INFO 2025-06-26 11:18:54,491 calibrate.py _nudge_pos():1806 [1] 906: 0.110 0.0037759 0.0042532 15805 52.68 10.646 14.961 2006-05-11T08:05:17.931432704 INFO 2025-06-26 11:18:54,537 calibrate.py _nudge_pos():1806 [1] 910: 0.110 0.0037577 0.0042681 15 0.05 11961.309 16948.589 2006-05-11T08:05:23.931021696 INFO 2025-06-26 11:18:55,211 calibrate.py _nudge_pos():1806 [1] 972: 0.110 0.0066775 0.0031007 15678 52.28 18.970 10.990 2006-05-11T08:58:41.931943680 INFO 2025-06-26 11:18:55,245 calibrate.py _nudge_pos():1806 [1] 975: 0.120 0.0059683 0.0045610 25 0.08 11081.073 10565.184 2006-05-11T08:58:48.931464192 INFO 2025-06-26 11:18:55,877 calibrate.py _nudge_pos():1806 [1] 1032: 0.110 0.0085758 0.0012539 15735 52.45 24.285 4.430 2006-05-11T09:52:11.932043520 INFO 2025-06-26 11:18:56,467 calibrate.py _nudge_pos():1806 [1] 1086: 0.120 0.0003370 0.0016223 5615 18.71 2.675 16.064 2006-05-11T10:11:47.931482112 INFO 2025-06-26 11:18:57,017 calibrate.py _nudge_pos():1806 [1] 1136: 0.120 0.0000185 -0.0000070 20 0.06 43.335 -20.436 2006-05-11T10:12:40.927851392 INFO 2025-06-26 11:18:57,062 calibrate.py _nudge_pos():1806 [1] 1140: 0.120 0.0048466 0.0011572 10670 35.56 20.239 6.029 2006-05-11T10:48:17.931456768 INFO 2025-06-26 11:18:57,698 calibrate.py _nudge_pos():1806 [1] 1197: 0.120 0.0000112 -0.0000160 15 0.05 35.657 -63.363 2006-05-11T10:49:16.927415424 INFO 2025-06-26 11:18:57,798 calibrate.py _nudge_pos():1806 [1] 1206: 0.120 0.0035394 0.0009723 10818 36.06 14.574 4.996 2006-05-11T11:25:28.928622976 INFO 2025-06-26 11:18:58,282 calibrate.py _nudge_pos():1806 [1] 1250: 0.130 0.0014006 0.0011485 11180 37.26 5.581 5.711 2006-05-11T12:03:27.932500608 INFO 2025-06-26 11:18:58,295 calibrate.py _nudge_pos():1806 [1] 1251: 0.140 0.0013172 0.0010248 485 1.61 121.238 117.707 2006-05-11T12:05:04.925856128 INFO 2025-06-26 11:18:58,928 calibrate.py _nudge_pos():1806 [1] 1309: 0.130 0.0000499 0.0023158 13190 43.96 0.168 9.761 2006-05-11T12:49:59.931235584 INFO 2025-06-26 11:18:59,685 calibrate.py _nudge_pos():1806 [1] 1378: 0.140 0.0000386 0.0021640 130 0.43 13.336 932.616 2006-05-11T12:51:33.924796544 INFO 2025-06-26 11:19:00,289 calibrate.py _nudge_pos():1806 [1] 1430: 0.140 0.0001179 0.0023464 10695 35.65 0.491 12.197 2006-05-11T13:28:04.924702592 INFO 2025-06-26 11:19:01,028 calibrate.py _nudge_pos():1806 [1] 1496: 0.140 0.0015458 0.0037356 13245 44.15 5.198 15.680 2006-05-11T14:13:18.928780800 INFO 2025-06-26 11:19:01,797 calibrate.py _nudge_pos():1806 [1] 1565: 0.140 0.0027749 0.0028290 12580 41.93 9.823 12.502 2006-05-11T14:56:22.931764352 INFO 2025-06-26 11:19:02,588 calibrate.py _nudge_pos():1806 [1] 1634: 0.150 0.0011108 0.0007931 4510 15.03 10.969 9.778 2006-05-11T15:12:32.925315328 INFO 2025-06-26 11:19:03,853 calibrate.py _nudge_pos():1806 [1] 1747: 0.150 0.0019650 0.0025150 10845 36.15 8.067 12.892 2006-05-11T15:50:33.929055872 INFO 2025-06-26 11:19:05,184 calibrate.py _nudge_pos():1806 [1] 1865: 0.170 0.0019378 0.0023139 8570 28.56 10.067 15.011 2006-05-11T16:21:04.923624064 INFO 2025-06-26 11:19:06,229 calibrate.py _nudge_pos():1862 [1] 1937: - - - 4983 16.61 - - INFO 2025-06-26 11:19:06,229 calibrate.py _nudge_pos():1868 [1] Points in final series = 336000 WARNING 2025-06-26 11:19:18,064 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:19:20,572 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:19:23,275 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:19:25,356 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:19:25,361 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.130.01/ctd1.nc INFO 2025-06-26 11:19:25,363 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 11:19:25,363 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 11:19:25,363 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:19:27,790 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:19:29,835 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:19:29,840 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.130.01/ctd2.nc INFO 2025-06-26 11:19:29,841 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 11:19:29,842 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 11:19:29,842 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:19:29,931 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:19:32,985 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 232560 805800 1036440 1037640 1037820 1038000 1038180 1039560 1040520 1262040 1263600 1495920 1607280 1607760 1608600 1610160 1718220 1720560 1724760 1725300 1831560 1831860 1832100 1833480 1836840 1949820 1953240 2064840 2065620 2175060 2176860 2179200 2179380 2290500 2531100 2633820 2745660 2747040 2747460 2747880 2862240 2972520 3108300 3108301 3108302 3108303 3108304 3108305 3108306 3108307 3108308 3108309 3108310 3108311 3108312 3108313 3108314 3108315 3108316 3108317 3108318 3108319 3108320 3108321 3108322 3108323 3108324 3108325 3108326 3108327 3108328 3108329 3108330 3108331 3108332 3108333 3108334 3108335 3108336 3108337 3108338 3108339 3108340 3108341 3108342 3108343 3108344 3108345 3198120 3199560 4001280 4001281 4001282] INFO 2025-06-26 11:19:33,682 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:19:33,689 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 11:19:33,690 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.130.01 ERROR 2025-06-26 11:19:33,690 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.130.01 INFO 2025-06-26 11:19:34,056 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_cal.nc INFO 2025-06-26 11:19:34,269 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 11:19:34,274 process.py align():251 [1] Alignment steps for 2006.130.01 INFO 2025-06-26 11:19:34,318 align.py process_cal():139 [1] Processing dorado_2006.130.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.130.01 INFO 2025-06-26 11:19:34,420 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:19:34,430 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:19:34,680 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:19:34,694 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:19:34,938 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:19:34,951 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:19:35,102 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:19:35,102 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:19:35,198 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:19:35,211 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:19:35,455 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:19:35,467 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:35,671 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:19:35,681 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:35,884 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:19:35,894 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:36,098 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:36,108 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:36,318 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:36,328 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:36,532 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:36,542 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:36,744 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:36,754 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:36,956 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:36,966 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:37,172 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:37,182 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:37,384 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:37,396 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:37,600 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:37,610 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:37,814 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:37,824 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:38,031 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:38,041 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:38,245 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:38,256 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:38,462 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:38,472 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:38,675 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:38,687 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:38,889 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:38,899 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:39,103 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:39,114 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:39,322 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:39,332 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:39,537 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.130.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:19:39,546 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:19:39,802 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 11:19:39,970 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 11:19:40,148 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 11:19:40,326 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:19:40,514 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:19:40,673 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_align.nc INFO 2025-06-26 11:19:40,834 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 11:19:40,837 process.py resample():273 [1] Resampling steps for 2006.130.01 INFO 2025-06-26 11:19:40,838 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:19:40,874 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_align.nc mission netCDF file INFO 2025-06-26 11:19:40,882 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_align.nc mission netCDF file INFO 2025-06-26 11:19:40,885 resample.py get_mission_start_end():1145 [1] navigation: 2006-05-10T21:59:08.542906496 to 2006-05-11T16:39:13.529049600 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 11:19:40,887 resample.py get_mission_start_end():1145 [1] hs2 : 2006-05-10T21:58:53.243954432 to 2006-05-11T16:39:13.549048192 (0 days 00:00:00.069995136 before mission_end) INFO 2025-06-26 11:19:40,890 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-05-10T21:59:16.622353024 to 2006-05-11T16:39:13.619043328 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:19:40,893 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-05-10T21:59:16.912333056 to 2006-05-11T16:39:13.409057792 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 11:19:40,895 resample.py get_mission_start_end():1145 [1] isus : 2006-05-10T22:00:14.978355456 to 2006-05-11T16:39:13.249068800 (0 days 00:00:00.369974528 before mission_end) INFO 2025-06-26 11:19:40,897 resample.py get_mission_start_end():1145 [1] biolume : 2006-05-10T21:58:47.304327296 to 2006-05-11T16:39:12.179107712 (0 days 00:00:01.439935616 before mission_end) INFO 2025-06-26 11:19:40,899 resample.py get_mission_start_end():1145 [1] tailcone : 2006-05-10T21:58:47.014381184 to 2006-05-11T16:39:13.619043328 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:19:40,900 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_align.nc mission netCDF file INFO 2025-06-26 11:19:40,901 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:41,563 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:41,672 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:41,777 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:41,882 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:41,976 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,070 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,159 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,247 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,330 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,414 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,498 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,581 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,665 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,748 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,831 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:42,914 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,003 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,094 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,182 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,271 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,359 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,448 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,481 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,508 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,533 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,566 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:43,666 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:19:44,143 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_1S.nc INFO 2025-06-26 11:19:46,315 create_products.py gulper_odv():401 [1] No gulper times found for 2006.130.01 INFO 2025-06-26 11:19:46,316 process.py archive():337 [1] Archiving steps for 2006.130.01 INFO 2025-06-26 11:19:46,316 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01, BASE_PATH = /data/auv_data INFO 2025-06-26 11:19:46,317 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:19:46,318 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.130.01_1S.nc INFO 2025-06-26 11:19:46,368 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:19:46,369 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.130.01_cal.nc INFO 2025-06-26 11:19:46,640 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:19:46,641 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.130.01_align.nc INFO 2025-06-26 11:19:46,884 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:19:46,956 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,025 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,030 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,079 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,293 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,303 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,401 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,460 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,637 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006130/2006.130.01 done. INFO 2025-06-26 11:19:47,637 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:19:47,637 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.130.01/dorado_2006.130.01_processing.log /Volumes/AUVCTD/surveys/2006/netcdf