INFO 2025-06-26 11:08:22,788 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 11:08:22,788 process.py process_mission():434 [1] dorado_info[mission]["comment"] = First unattended mission done overnight! Multiple transects in this one mission fileCore dumps on _2column.png with headless print - 18 July 2007 - ctdToUse = ctd1 INFO 2025-06-26 11:08:22,788 process.py process_mission():449 [1] Processing AUVCTD mission 2006.065.12 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:08:22,788 process.py download_process():165 [1] Download and processing steps for 2006.065.12 INFO 2025-06-26 11:08:22,788 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006065/2006.065.12 INFO 2025-06-26 11:08:22,789 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006065/2006.065.12 to /data/auv_data/dorado/missionlogs/2006.065.12 INFO 2025-06-26 11:08:29,128 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.065.12 INFO 2025-06-26 11:08:29,130 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/ctdDriver.log (23822963 bytes) INFO 2025-06-26 11:08:30,919 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/ctdDriver2.log (23822517 bytes) INFO 2025-06-26 11:08:32,654 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/gps.log (382172 bytes) INFO 2025-06-26 11:08:32,702 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/hydroscatlog.log (16240454 bytes) INFO 2025-06-26 11:08:34,611 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/navigation.log (79864650 bytes) INFO 2025-06-26 11:08:40,316 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/isuslog.log (1354645 bytes) INFO 2025-06-26 11:08:40,447 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/parosci.log (34822694 bytes) INFO 2025-06-26 11:08:43,425 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.065.12/parosci.log: [220475 220477 220478] INFO 2025-06-26 11:08:43,545 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/tailCone.log (16248043 bytes) INFO 2025-06-26 11:08:45,542 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.065.12/biolume.log (18419980 bytes) INFO 2025-06-26 11:08:47,294 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:08:48,214 logs2netcdfs.py download_process_logs():807 [1] Time to process: 19.08 seconds WARNING 2025-06-26 11:08:48,215 process.py download_process():196 [1] No lopc.bin file for 2006.065.12 INFO 2025-06-26 11:08:48,215 process.py calibrate():227 [1] Calibration steps for 2006.065.12 INFO 2025-06-26 11:08:48,739 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 11:08:48,741 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:08:49,479 calibrate.py _nudge_pos():1806 [1] 88: 0.110 -0.0017907 -0.0005513 4725 15.75 -16.879 -6.488 2006-03-06T21:14:23.953305472 INFO 2025-06-26 11:08:49,870 calibrate.py _nudge_pos():1806 [1] 126: 0.090 -0.0003125 0.0004308 4525 15.08 -3.076 5.293 2006-03-06T21:30:05.958773632 INFO 2025-06-26 11:08:50,542 calibrate.py _nudge_pos():1806 [1] 191: 0.100 -0.0008952 0.0010119 11410 38.03 -3.494 4.931 2006-03-06T22:09:11.958061696 INFO 2025-06-26 11:08:51,220 calibrate.py _nudge_pos():1806 [1] 256: 0.110 -0.0017780 0.0005194 11590 38.63 -6.833 2.492 2006-03-06T22:48:53.954883840 INFO 2025-06-26 11:08:51,717 calibrate.py _nudge_pos():1806 [1] 304: 0.100 -0.0010863 0.0009439 10895 36.31 -4.441 4.816 2006-03-06T23:25:59.962391808 INFO 2025-06-26 11:08:51,783 calibrate.py _nudge_pos():1806 [1] 310: 0.100 0.0000182 0.0000186 40 0.13 20.826 26.533 2006-03-06T23:26:12.961501312 INFO 2025-06-26 11:08:52,497 calibrate.py _nudge_pos():1806 [1] 378: 0.120 -0.0002730 0.0006120 11685 38.95 -1.041 2.912 2006-03-07T00:06:17.956747776 INFO 2025-06-26 11:08:53,065 calibrate.py _nudge_pos():1806 [1] 431: 0.100 -0.0000028 -0.0000078 30 0.10 -4.357 -15.015 2006-03-07T00:07:15.952774784 INFO 2025-06-26 11:08:53,098 calibrate.py _nudge_pos():1806 [1] 434: 0.110 -0.0004508 0.0009604 11880 39.60 -1.691 4.495 2006-03-07T00:46:53.959870080 INFO 2025-06-26 11:08:53,153 calibrate.py _nudge_pos():1806 [1] 439: 0.110 -0.0000066 0.0000174 25 0.08 -12.269 40.362 2006-03-07T00:47:02.959253504 INFO 2025-06-26 11:08:53,455 calibrate.py _nudge_pos():1806 [1] 468: 0.100 0.0000103 0.0000077 15 0.05 32.657 30.636 2006-03-07T00:47:33.957130240 INFO 2025-06-26 11:08:53,764 calibrate.py _nudge_pos():1806 [1] 497: 0.120 -0.0006268 0.0024317 12435 41.45 -2.246 10.872 2006-03-07T01:29:29.954772480 INFO 2025-06-26 11:08:54,293 calibrate.py _nudge_pos():1806 [1] 547: 0.110 0.0000643 0.0000560 50 0.16 58.448 63.497 2006-03-07T01:30:28.960730368 INFO 2025-06-26 11:08:54,325 calibrate.py _nudge_pos():1806 [1] 550: 0.120 -0.0020209 0.0039736 11930 39.76 -7.548 18.517 2006-03-07T02:10:17.957073024 INFO 2025-06-26 11:08:54,909 calibrate.py _nudge_pos():1806 [1] 604: 0.110 0.0059445 0.0035666 10655 35.51 24.858 18.610 2006-03-07T02:46:41.957458560 INFO 2025-06-26 11:08:55,480 calibrate.py _nudge_pos():1806 [1] 657: 0.140 0.0068136 0.0025595 10685 35.61 28.410 13.317 2006-03-07T03:23:11.957433216 INFO 2025-06-26 11:08:55,988 calibrate.py _nudge_pos():1806 [1] 704: 0.140 0.0067448 0.0008902 10915 36.38 27.529 4.534 2006-03-07T04:00:20.954736512 INFO 2025-06-26 11:08:56,176 calibrate.py _nudge_pos():1806 [1] 721: 0.130 0.0000213 -0.0000177 15 0.05 67.892 -70.151 2006-03-07T04:00:39.953435008 INFO 2025-06-26 11:08:56,696 calibrate.py _nudge_pos():1806 [1] 769: 0.120 0.0054317 0.0006553 10785 35.95 22.435 3.378 2006-03-07T04:37:23.962450048 INFO 2025-06-26 11:08:57,274 calibrate.py _nudge_pos():1806 [1] 822: 0.130 0.0049123 0.0012210 10690 35.63 20.468 6.350 2006-03-07T05:13:53.962424704 INFO 2025-06-26 11:08:57,765 calibrate.py _nudge_pos():1806 [1] 867: 0.130 0.0032250 0.0015425 10880 36.26 13.201 7.882 2006-03-07T05:50:53.960344576 INFO 2025-06-26 11:08:58,285 calibrate.py _nudge_pos():1806 [1] 915: 0.130 0.0038516 0.0016042 11555 38.51 14.844 7.718 2006-03-07T06:30:11.958810624 INFO 2025-06-26 11:08:58,826 calibrate.py _nudge_pos():1806 [1] 965: 0.140 0.0011673 0.0008170 4705 15.68 11.049 9.655 2006-03-07T06:46:41.960990720 INFO 2025-06-26 11:08:59,663 calibrate.py _nudge_pos():1806 [1] 1043: 0.140 -0.0001295 0.0009889 6700 22.33 -0.861 8.206 2006-03-07T07:10:18.953920128 INFO 2025-06-26 11:09:00,300 calibrate.py _nudge_pos():1806 [1] 1100: 0.150 -0.0017765 0.0014789 11720 39.06 -6.751 7.015 2006-03-07T07:50:18.959508480 INFO 2025-06-26 11:09:00,974 calibrate.py _nudge_pos():1806 [1] 1162: 0.140 -0.0018626 0.0012272 10850 36.16 -7.646 6.288 2006-03-07T08:27:29.956674560 INFO 2025-06-26 11:09:01,564 calibrate.py _nudge_pos():1806 [1] 1216: 0.140 0.0003392 0.0004105 11105 37.01 1.360 2.055 2006-03-07T09:05:23.960894848 INFO 2025-06-26 11:09:02,083 calibrate.py _nudge_pos():1806 [1] 1263: 0.170 0.0011301 0.0003542 11830 39.43 4.256 1.665 2006-03-07T09:45:35.955661824 INFO 2025-06-26 11:09:02,703 calibrate.py _nudge_pos():1806 [1] 1319: 0.160 0.0005900 0.0015016 11725 39.08 2.242 7.120 2006-03-07T10:25:35.961250048 INFO 2025-06-26 11:09:03,268 calibrate.py _nudge_pos():1806 [1] 1370: 0.160 0.0000457 0.0000291 30 0.10 70.273 55.697 2006-03-07T10:26:31.957414144 INFO 2025-06-26 11:09:03,444 calibrate.py _nudge_pos():1806 [1] 1386: 0.170 -0.0015197 0.0028468 11825 39.41 -5.726 13.384 2006-03-07T11:06:11.954373120 INFO 2025-06-26 11:09:04,223 calibrate.py _nudge_pos():1806 [1] 1456: 0.170 -0.0030502 0.0038733 11775 39.25 -11.542 18.287 2006-03-07T11:46:35.958317568 INFO 2025-06-26 11:09:04,947 calibrate.py _nudge_pos():1806 [1] 1522: 0.170 0.0043549 0.0031360 11225 37.41 17.286 15.532 2006-03-07T12:25:05.960071552 INFO 2025-06-26 11:09:05,439 calibrate.py _nudge_pos():1806 [1] 1566: 0.190 0.0032622 0.0022702 10950 36.50 13.273 11.526 2006-03-07T13:02:18.957100928 INFO 2025-06-26 11:09:06,116 calibrate.py _nudge_pos():1806 [1] 1624: 0.180 0.0033695 0.0013689 10725 35.75 13.996 7.096 2006-03-07T13:39:00.956253568 INFO 2025-06-26 11:09:06,675 calibrate.py _nudge_pos():1806 [1] 1674: 0.180 0.0030710 0.0005649 10880 36.26 12.574 2.887 2006-03-07T14:16:05.953830656 INFO 2025-06-26 11:09:07,267 calibrate.py _nudge_pos():1806 [1] 1727: 0.190 0.0021118 -0.0012874 8740 29.13 10.764 -8.189 2006-03-07T14:46:05.960521984 INFO 2025-06-26 11:09:47,657 calibrate.py _nudge_pos():1862 [1] 5274: - - - 0 0.00 - - INFO 2025-06-26 11:09:47,657 calibrate.py _nudge_pos():1868 [1] Points in final series = 337404 WARNING 2025-06-26 11:09:59,371 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:10:01,866 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:10:04,574 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:10:06,629 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:10:06,634 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.065.12/ctd1.nc INFO 2025-06-26 11:10:06,636 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 11:10:06,636 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 11:10:06,636 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:10:09,118 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:10:11,172 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:10:11,177 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.065.12/ctd2.nc INFO 2025-06-26 11:10:11,179 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 11:10:11,179 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 11:10:11,179 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:10:11,269 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:10:14,341 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 10020 10140 10380 10500 11280 11820 12480 12660 13260 13440 13860 16740 123540 123960 124080 125400 126780 126960 127380 127920 128160 237480 239100 261240 261241 261242 261243 403860 462540 464280 465480 466620 577680 804180 919560 919740 919920 1027920 1029660 1144020 1146060 1147800 1255260 1368660 1488600 1489080 1526940 1595760 1824900 1826520 1827540 1830360 1831020 1941420 1943580 1945140 2055900 2285520 2286600 2396280 2397840 2506500 2847900 3303540 3741720 3741721] INFO 2025-06-26 11:10:14,969 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:10:14,976 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 11:10:14,978 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.065.12 ERROR 2025-06-26 11:10:14,978 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.065.12 INFO 2025-06-26 11:10:15,244 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_cal.nc INFO 2025-06-26 11:10:15,450 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 11:10:15,455 process.py align():251 [1] Alignment steps for 2006.065.12 INFO 2025-06-26 11:10:15,498 align.py process_cal():139 [1] Processing dorado_2006.065.12_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.065.12 INFO 2025-06-26 11:10:15,598 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:10:15,608 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:10:15,853 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:10:15,867 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:10:16,126 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:10:16,138 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:10:16,283 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:10:16,283 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:10:16,378 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:10:16,391 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:10:16,616 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:10:16,626 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:16,824 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:10:16,833 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:17,033 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:10:17,043 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:17,239 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:17,249 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:17,446 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:17,457 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:17,656 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:17,666 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:17,862 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:17,871 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:18,081 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:18,091 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:18,287 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:18,296 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:18,500 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:18,510 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:18,711 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:18,720 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:18,925 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:18,934 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:19,141 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:19,150 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:19,351 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:19,361 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:19,562 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:19,572 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:19,775 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:19,786 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:19,986 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:19,996 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:20,238 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:20,252 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:20,463 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:20,473 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:20,670 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.065.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:10:20,680 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:10:20,940 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:10:21,103 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:10:21,264 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:10:21,432 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:10:21,614 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:10:21,765 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_align.nc INFO 2025-06-26 11:10:21,921 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 11:10:21,924 process.py resample():273 [1] Resampling steps for 2006.065.12 INFO 2025-06-26 11:10:21,925 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:10:21,958 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_align.nc mission netCDF file INFO 2025-06-26 11:10:21,967 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_align.nc mission netCDF file INFO 2025-06-26 11:10:21,969 resample.py get_mission_start_end():1145 [1] navigation: 2006-03-06T20:57:34.172480128 to 2006-03-07T15:45:34.156083584 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:10:21,972 resample.py get_mission_start_end():1145 [1] hs2 : 2006-03-06T20:57:16.113717376 to 2006-03-07T15:45:34.126085760 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 11:10:21,974 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-03-06T20:57:38.932154240 to 2006-03-07T15:45:34.126085760 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 11:10:21,977 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-03-06T20:57:39.132140416 to 2006-03-07T15:45:34.086088448 (0 days 00:00:00.069995136 before mission_end) INFO 2025-06-26 11:10:21,979 resample.py get_mission_start_end():1145 [1] isus : 2006-03-06T20:58:41.937837824 to 2006-03-07T15:45:33.486129536 (0 days 00:00:00.669954048 before mission_end) INFO 2025-06-26 11:10:21,980 resample.py get_mission_start_end():1145 [1] biolume : 2006-03-06T20:57:11.274014464 to 2006-03-07T15:45:33.116120576 (0 days 00:00:01.039963008 before mission_end) INFO 2025-06-26 11:10:21,983 resample.py get_mission_start_end():1145 [1] tailcone : 2006-03-06T20:57:11.734017408 to 2006-03-07T15:45:34.086088448 (0 days 00:00:00.069995136 before mission_end) INFO 2025-06-26 11:10:21,984 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_align.nc mission netCDF file INFO 2025-06-26 11:10:21,984 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:22,660 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:22,767 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:22,872 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:22,978 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,069 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,162 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,254 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,344 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,433 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,523 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,610 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,698 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,785 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,871 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:23,957 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,045 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,135 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,224 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,312 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,403 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,489 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,576 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,608 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,636 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,661 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,701 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:24,803 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:10:25,284 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_1S.nc INFO 2025-06-26 11:10:28,899 create_products.py gulper_odv():401 [1] No gulper times found for 2006.065.12 INFO 2025-06-26 11:10:28,899 process.py archive():337 [1] Archiving steps for 2006.065.12 INFO 2025-06-26 11:10:28,899 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12, BASE_PATH = /data/auv_data INFO 2025-06-26 11:10:28,901 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:10:28,902 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.065.12_1S.nc INFO 2025-06-26 11:10:28,952 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:10:28,953 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.065.12_cal.nc INFO 2025-06-26 11:10:29,240 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:10:29,241 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.065.12_align.nc INFO 2025-06-26 11:10:29,498 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:10:29,573 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:29,640 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:29,646 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:29,691 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:29,882 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:29,892 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:29,997 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:30,052 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:30,240 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006065/2006.065.12 done. INFO 2025-06-26 11:10:30,241 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:10:30,241 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.065.12/dorado_2006.065.12_processing.log /Volumes/AUVCTD/surveys/2006/netcdf