INFO 2025-06-26 11:16:06,870 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 11:16:06,870 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Unattended BIOLUME mission - Monterey to Soquel, then sawtooth at canyon edge back to M0 - ctdToUse = ctd1 INFO 2025-06-26 11:16:06,871 process.py process_mission():449 [1] Processing BIOLUME mission 2006.117.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:16:06,871 process.py download_process():165 [1] Download and processing steps for 2006.117.05 INFO 2025-06-26 11:16:06,871 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006117/2006.117.05 INFO 2025-06-26 11:16:06,871 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006117/2006.117.05 to /data/auv_data/dorado/missionlogs/2006.117.05 INFO 2025-06-26 11:16:12,533 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.117.05 INFO 2025-06-26 11:16:12,533 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/ctdDriver.log (18719051 bytes) INFO 2025-06-26 11:16:13,918 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/ctdDriver2.log (18718957 bytes) INFO 2025-06-26 11:16:15,264 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/gps.log (127364 bytes) INFO 2025-06-26 11:16:15,287 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/hydroscatlog.log (12760694 bytes) INFO 2025-06-26 11:16:16,791 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/navigation.log (62743794 bytes) INFO 2025-06-26 11:16:21,252 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/isuslog.log (1146197 bytes) INFO 2025-06-26 11:16:21,363 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/parosci.log (27309350 bytes) INFO 2025-06-26 11:16:23,546 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.117.05/parosci.log: [568932] INFO 2025-06-26 11:16:23,612 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/tailCone.log (12766363 bytes) INFO 2025-06-26 11:16:25,206 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.117.05/biolume.log (14473804 bytes) INFO 2025-06-26 11:16:26,568 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:16:27,280 logs2netcdfs.py download_process_logs():807 [1] Time to process: 14.75 seconds WARNING 2025-06-26 11:16:27,280 process.py download_process():196 [1] No lopc.bin file for 2006.117.05 INFO 2025-06-26 11:16:27,280 process.py calibrate():227 [1] Calibration steps for 2006.117.05 INFO 2025-06-26 11:16:27,632 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 11:16:27,634 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:16:29,311 calibrate.py _nudge_pos():1806 [1] 184: 0.180 -0.0003958 0.0005364 2389 7.96 -7.391 12.481 2006-04-27T03:29:53.841995520 INFO 2025-06-26 11:16:29,853 calibrate.py _nudge_pos():1806 [1] 238: 0.180 -0.0012800 -0.0010477 5765 19.21 -9.905 -10.104 2006-04-27T03:49:59.839379072 INFO 2025-06-26 11:16:30,367 calibrate.py _nudge_pos():1806 [1] 289: 0.200 -0.0026378 -0.0020569 10123 33.76 -11.613 -11.289 2006-04-27T04:24:35.837163392 INFO 2025-06-26 11:16:30,922 calibrate.py _nudge_pos():1806 [1] 344: 0.190 -0.0029327 -0.0020543 10650 35.50 -12.277 -10.724 2006-04-27T05:00:59.837549184 INFO 2025-06-26 11:16:31,034 calibrate.py _nudge_pos():1806 [1] 355: 0.190 -0.0000125 -0.0000040 45 0.15 -12.706 -5.047 2006-04-27T05:01:18.836247680 INFO 2025-06-26 11:16:31,598 calibrate.py _nudge_pos():1806 [1] 411: 0.190 -0.0031804 -0.0021471 10880 36.26 -13.029 -10.971 2006-04-27T05:38:29.843413120 INFO 2025-06-26 11:16:31,650 calibrate.py _nudge_pos():1806 [1] 416: 0.190 -0.0000229 -0.0000387 30 0.10 -35.175 -74.149 2006-04-27T05:38:39.842728192 INFO 2025-06-26 11:16:32,256 calibrate.py _nudge_pos():1806 [1] 475: 0.190 -0.0037830 -0.0020461 10880 36.26 -15.493 -10.455 2006-04-27T06:15:53.839688960 INFO 2025-06-26 11:16:32,840 calibrate.py _nudge_pos():1806 [1] 533: 0.190 -0.0022482 -0.0009592 6585 21.95 -15.210 -8.099 2006-04-27T06:38:47.845563136 INFO 2025-06-26 11:16:33,359 calibrate.py _nudge_pos():1806 [1] 584: 0.200 -0.0009644 -0.0005237 4070 13.56 -10.556 -7.155 2006-04-27T06:53:11.836375680 INFO 2025-06-26 11:16:33,854 calibrate.py _nudge_pos():1806 [1] 633: 0.200 -0.0022061 0.0017268 8669 28.89 -11.333 11.074 2006-04-27T07:22:53.844299776 INFO 2025-06-26 11:16:33,915 calibrate.py _nudge_pos():1806 [1] 639: 0.190 0.0000266 0.0000048 55 0.18 21.944 4.897 2006-04-27T07:23:09.843203840 INFO 2025-06-26 11:16:34,518 calibrate.py _nudge_pos():1806 [1] 698: 0.010 -0.0019432 0.0010959 6531 21.77 -13.248 9.330 2006-04-27T07:45:54.039749888 INFO 2025-06-26 11:16:35,045 calibrate.py _nudge_pos():1806 [1] 749: 0.010 -0.0041974 0.0026163 10940 36.46 -17.075 13.296 2006-04-27T08:23:12.036436608 INFO 2025-06-26 11:16:35,500 calibrate.py _nudge_pos():1806 [1] 793: 0.010 -0.0043002 0.0026698 11005 36.68 -17.384 13.488 2006-04-27T09:00:36.042711680 INFO 2025-06-26 11:16:36,037 calibrate.py _nudge_pos():1806 [1] 845: 0.020 -0.0043181 0.0023899 10665 35.55 -18.006 12.458 2006-04-27T09:37:00.043097216 INFO 2025-06-26 11:16:36,091 calibrate.py _nudge_pos():1806 [1] 850: 0.010 0.0000223 -0.0000464 55 0.18 18.389 -47.803 2006-04-27T09:37:15.042069888 INFO 2025-06-26 11:16:36,599 calibrate.py _nudge_pos():1806 [1] 899: 0.010 -0.0045038 0.0022047 10545 35.15 -18.987 11.623 2006-04-27T10:13:12.044305024 INFO 2025-06-26 11:16:37,136 calibrate.py _nudge_pos():1806 [1] 949: 0.010 -0.0031506 0.0016806 7765 25.88 -18.033 12.033 2006-04-27T10:39:54.044560640 INFO 2025-06-26 11:16:37,667 calibrate.py _nudge_pos():1806 [1] 1000: 0.010 -0.0006776 0.0006948 2720 9.06 -11.075 14.204 2006-04-27T10:49:48.043868800 INFO 2025-06-26 11:16:38,457 calibrate.py _nudge_pos():1806 [1] 1076: 0.020 -0.0036997 0.0019688 12225 40.75 -13.454 8.954 2006-04-27T11:31:48.041237120 INFO 2025-06-26 11:16:39,032 calibrate.py _nudge_pos():1806 [1] 1131: 0.020 -0.0036710 0.0014727 12390 41.30 -13.177 6.608 2006-04-27T12:14:00.037783680 INFO 2025-06-26 11:16:39,521 calibrate.py _nudge_pos():1806 [1] 1178: 0.030 -0.0048840 0.0012586 12970 43.23 -16.753 5.395 2006-04-27T12:58:00.036931328 INFO 2025-06-26 11:16:40,148 calibrate.py _nudge_pos():1806 [1] 1235: 0.040 -0.0046685 0.0005271 13220 44.06 -15.717 2.216 2006-04-27T13:43:00.041968128 INFO 2025-06-26 11:16:40,838 calibrate.py _nudge_pos():1806 [1] 1300: 0.030 -0.0004049 -0.0006772 9130 30.43 -1.974 -4.124 2006-04-27T14:14:30.042494336 INFO 2025-06-26 11:16:41,316 calibrate.py _nudge_pos():1806 [1] 1345: 0.030 0.0001974 -0.0012810 8925 29.75 0.985 -7.980 2006-04-27T14:45:00.037131008 INFO 2025-06-26 11:16:41,402 calibrate.py _nudge_pos():1806 [1] 1353: 0.040 -0.0000142 0.0000058 15 0.05 -45.291 22.984 2006-04-27T14:45:10.036446080 INFO 2025-06-26 11:16:41,931 calibrate.py _nudge_pos():1806 [1] 1403: 0.040 -0.0022011 0.0024499 11043 36.81 -8.871 12.331 2006-04-27T15:22:48.041762176 INFO 2025-06-26 11:16:42,430 calibrate.py _nudge_pos():1806 [1] 1450: 0.040 -0.0025854 0.0013025 7318 24.40 -15.720 9.893 2006-04-27T15:47:58.038320256 INFO 2025-06-26 11:16:43,247 calibrate.py _nudge_pos():1806 [1] 1526: 0.040 -0.0006584 -0.0006412 8695 28.98 -3.371 -4.100 2006-04-27T16:18:12.044052352 INFO 2025-06-26 11:16:43,846 calibrate.py _nudge_pos():1806 [1] 1582: 0.040 0.0004368 -0.0025723 10165 33.88 1.914 -14.069 2006-04-27T16:53:00.041014656 INFO 2025-06-26 11:16:44,443 calibrate.py _nudge_pos():1806 [1] 1638: 0.040 -0.0037256 0.0021380 12115 40.38 -13.689 9.811 2006-04-27T17:34:18.041260032 INFO 2025-06-26 11:16:45,021 calibrate.py _nudge_pos():1806 [1] 1692: 0.060 -0.0031012 0.0012996 8765 29.21 -15.747 8.243 2006-04-27T18:04:24.037540864 INFO 2025-06-26 11:16:45,719 calibrate.py _nudge_pos():1862 [1] 1735: - - - 3 0.01 - - INFO 2025-06-26 11:16:45,720 calibrate.py _nudge_pos():1868 [1] Points in final series = 265698 WARNING 2025-06-26 11:16:54,913 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:16:56,898 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:16:59,026 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:17:00,651 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:17:00,654 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.117.05/ctd1.nc INFO 2025-06-26 11:17:00,656 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 11:17:00,656 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 11:17:00,656 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:17:02,563 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:17:04,168 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:17:04,172 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.117.05/ctd2.nc INFO 2025-06-26 11:17:04,174 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 11:17:04,174 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 11:17:04,174 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:17:04,247 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:17:06,659 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 600 601 602 603 63000 66600 291300 519000 520020 521520 521700 522300 631500 632460 632820 637020 639360 859500 1201140 1772760] INFO 2025-06-26 11:17:07,140 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:17:07,147 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 11:17:07,147 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.117.05 ERROR 2025-06-26 11:17:07,147 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.117.05 INFO 2025-06-26 11:17:07,348 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_cal.nc INFO 2025-06-26 11:17:07,526 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 11:17:07,532 process.py align():251 [1] Alignment steps for 2006.117.05 INFO 2025-06-26 11:17:07,570 align.py process_cal():139 [1] Processing dorado_2006.117.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.117.05 INFO 2025-06-26 11:17:07,649 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:17:07,657 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:17:07,854 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:17:07,865 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:17:08,060 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:17:08,071 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:17:08,189 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:17:08,189 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:17:08,262 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:17:08,272 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:17:08,461 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:17:08,469 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:08,636 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:17:08,645 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:08,804 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:17:08,813 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:08,979 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:08,988 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:09,155 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:09,164 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:09,323 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:09,331 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:09,492 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:09,501 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:09,666 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:09,675 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:09,833 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:09,842 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:10,007 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:10,017 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:10,183 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:10,191 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:10,358 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:10,366 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:10,535 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:10,544 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:10,710 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:10,719 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:10,878 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:10,887 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:11,054 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:11,065 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:11,231 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:11,239 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:11,405 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:11,413 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:11,578 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:11,588 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:11,752 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.117.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:17:11,760 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:17:11,963 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 11:17:12,095 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 11:17:12,224 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 11:17:12,363 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:17:12,510 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:17:12,637 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_align.nc INFO 2025-06-26 11:17:12,774 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 11:17:12,777 process.py resample():273 [1] Resampling steps for 2006.117.05 INFO 2025-06-26 11:17:12,777 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:17:12,809 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_align.nc mission netCDF file INFO 2025-06-26 11:17:12,816 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_align.nc mission netCDF file INFO 2025-06-26 11:17:12,818 resample.py get_mission_start_end():1145 [1] navigation: 2006-04-27T03:19:15.245742336 to 2006-04-27T18:05:28.643115008 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:17:12,821 resample.py get_mission_start_end():1145 [1] hs2 : 2006-04-27T03:18:57.306971264 to 2006-04-27T18:05:28.583119104 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 11:17:12,823 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-04-27T03:19:12.425935488 to 2006-04-27T18:05:28.413130752 (0 days 00:00:00.229984256 before mission_end) INFO 2025-06-26 11:17:12,825 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-04-27T03:19:12.445934080 to 2006-04-27T18:05:28.463127424 (0 days 00:00:00.179987584 before mission_end) INFO 2025-06-26 11:17:12,827 resample.py get_mission_start_end():1145 [1] isus : 2006-04-27T03:20:21.711189248 to 2006-04-27T18:05:28.613117184 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 11:17:12,829 resample.py get_mission_start_end():1145 [1] biolume : 2006-04-27T03:18:52.507265792 to 2006-04-27T18:05:27.863134336 (0 days 00:00:00.779980672 before mission_end) INFO 2025-06-26 11:17:12,831 resample.py get_mission_start_end():1145 [1] tailcone : 2006-04-27T03:18:53.297245952 to 2006-04-27T18:05:28.353134848 (0 days 00:00:00.289980160 before mission_end) INFO 2025-06-26 11:17:12,832 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_align.nc mission netCDF file INFO 2025-06-26 11:17:12,833 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,374 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,462 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,548 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,635 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,711 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,787 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,862 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:13,936 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,004 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,072 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,140 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,208 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,275 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,342 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,410 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,477 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,548 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,619 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,691 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,763 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,897 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,969 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:14,996 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:15,023 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:15,046 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:15,073 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:15,155 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:17:15,559 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_1S.nc INFO 2025-06-26 11:17:18,007 create_products.py gulper_odv():401 [1] No gulper times found for 2006.117.05 INFO 2025-06-26 11:17:18,007 process.py archive():337 [1] Archiving steps for 2006.117.05 INFO 2025-06-26 11:17:18,007 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05, BASE_PATH = /data/auv_data INFO 2025-06-26 11:17:18,009 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:17:18,010 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.117.05_1S.nc INFO 2025-06-26 11:17:18,049 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:17:18,050 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.117.05_cal.nc INFO 2025-06-26 11:17:18,277 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:17:18,278 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.117.05_align.nc INFO 2025-06-26 11:17:18,504 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:17:18,565 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:18,625 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:18,632 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:18,673 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:18,863 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:18,872 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:18,954 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:19,014 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:19,168 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006117/2006.117.05 done. INFO 2025-06-26 11:17:19,169 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:17:19,170 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.117.05/dorado_2006.117.05_processing.log /Volumes/AUVCTD/surveys/2006/netcdf