INFO 2025-06-26 10:30:46,535 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 10:30:46,536 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Elkhorn Slough plume racetrack Monterey triangle (missing short mission 01) - ctdToUse = ctd1 INFO 2025-06-26 10:30:46,536 process.py process_mission():449 [1] Processing BIOLUME mission 2005.020.04 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:30:46,536 process.py download_process():165 [1] Download and processing steps for 2005.020.04 INFO 2025-06-26 10:30:46,536 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005020/2005.020.04 INFO 2025-06-26 10:30:46,536 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005020/2005.020.04 to /data/auv_data/dorado/missionlogs/2005.020.04 INFO 2025-06-26 10:30:46,961 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.020.04 INFO 2025-06-26 10:30:46,961 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/ctdDriver.log (4355867 bytes) INFO 2025-06-26 10:30:47,284 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/ctdDriver2.log (4359293 bytes) INFO 2025-06-26 10:30:47,606 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/gps.log (46364 bytes) INFO 2025-06-26 10:30:47,619 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/hydroscatlog.log (2974574 bytes) INFO 2025-06-26 10:30:47,972 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.020.04/hydroscatlog.log: [44684] INFO 2025-06-26 10:30:47,979 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/navigation.log (14608054 bytes) INFO 2025-06-26 10:30:49,037 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/isuslog.log (51317 bytes) INFO 2025-06-26 10:30:49,047 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/parosci.log (2921222 bytes) INFO 2025-06-26 10:30:49,290 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/tailCone.log (2975851 bytes) INFO 2025-06-26 10:30:49,655 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.020.04/biolume.log (3376204 bytes) INFO 2025-06-26 10:30:49,980 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:30:50,155 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.19 seconds WARNING 2025-06-26 10:30:50,156 process.py download_process():196 [1] No lopc.bin file for 2005.020.04 INFO 2025-06-26 10:30:50,156 process.py calibrate():227 [1] Calibration steps for 2005.020.04 INFO 2025-06-26 10:30:50,294 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 10:30:50,296 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:30:50,994 calibrate.py _nudge_pos():1806 [1] 91: 0.150 -0.0000402 0.0000029 125 0.41 -14.432 1.304 2005-01-20T18:09:03.597363200 INFO 2025-06-26 10:30:51,045 calibrate.py _nudge_pos():1806 [1] 96: 0.150 -0.0004917 0.0003259 4345 14.48 -5.039 4.171 2005-01-20T18:23:36.597558528 INFO 2025-06-26 10:30:51,542 calibrate.py _nudge_pos():1806 [1] 149: 0.140 -0.0040782 0.0003074 8380 27.93 -21.661 2.040 2005-01-20T18:52:24.599182336 INFO 2025-06-26 10:30:51,990 calibrate.py _nudge_pos():1806 [1] 197: 0.140 -0.0010583 -0.0009420 6365 21.21 -7.402 -8.228 2005-01-20T19:14:24.598756096 INFO 2025-06-26 10:30:52,432 calibrate.py _nudge_pos():1806 [1] 244: 0.150 -0.0005779 0.0003586 4900 16.33 -5.252 4.070 2005-01-20T19:31:30.598470400 INFO 2025-06-26 10:30:53,052 calibrate.py _nudge_pos():1806 [1] 309: 0.150 -0.0041492 0.0004361 7929 26.43 -23.288 3.058 2005-01-20T19:59:00.595437824 INFO 2025-06-26 10:30:53,072 calibrate.py _nudge_pos():1806 [1] 311: 0.160 -0.0041193 0.0004054 30 0.10 -6321.944 777.181 2005-01-20T19:59:07.594958336 INFO 2025-06-26 10:30:53,587 calibrate.py _nudge_pos():1806 [1] 365: 0.130 -0.0010902 -0.0008454 6509 21.70 -7.455 -7.220 2005-01-20T20:21:42.602134016 INFO 2025-06-26 10:30:54,082 calibrate.py _nudge_pos():1806 [1] 414: 0.160 -0.0000288 0.0000118 275 0.91 -4.676 2.389 2005-01-20T20:23:25.595078528 INFO 2025-06-26 10:30:54,142 calibrate.py _nudge_pos():1806 [1] 420: 0.150 -0.0004839 0.0003187 4740 15.80 -4.545 3.738 2005-01-20T20:39:18.599793152 INFO 2025-06-26 10:30:54,807 calibrate.py _nudge_pos():1806 [1] 488: 0.150 -0.0042149 0.0003230 7885 26.28 -23.792 2.277 2005-01-20T21:06:42.597171840 INFO 2025-06-26 10:30:54,827 calibrate.py _nudge_pos():1806 [1] 490: 0.150 -0.0042134 0.0003278 55 0.18 -3472.682 337.522 2005-01-20T21:06:54.596349696 INFO 2025-06-26 10:30:55,288 calibrate.py _nudge_pos():1806 [1] 538: 0.160 -0.0010639 -0.0008353 6365 21.21 -7.442 -7.297 2005-01-20T21:28:54.595923456 INFO 2025-06-26 10:30:55,693 calibrate.py _nudge_pos():1806 [1] 580: 0.150 0.0000257 0.0000020 25 0.08 47.608 4.622 2005-01-20T21:29:40.602771712 INFO 2025-06-26 10:30:55,713 calibrate.py _nudge_pos():1806 [1] 582: 0.150 -0.0000060 0.0000524 30 0.10 -9.247 100.426 2005-01-20T21:29:47.602292352 INFO 2025-06-26 10:30:55,838 calibrate.py _nudge_pos():1806 [1] 595: 0.140 -0.0001096 0.0000029 965 3.21 -5.062 0.166 2005-01-20T21:33:12.598249216 INFO 2025-06-26 10:30:56,188 calibrate.py _nudge_pos():1862 [1] 610: - - - 1 0.00 - - INFO 2025-06-26 10:30:56,188 calibrate.py _nudge_pos():1868 [1] Points in final series = 61889 WARNING 2025-06-26 10:30:56,238 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 10:31:02,849 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:03,308 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:03,675 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:03,677 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.020.04/ctd1.nc INFO 2025-06-26 10:31:03,679 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 10:31:03,679 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 10:31:03,679 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:31:04,128 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 16 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:04,501 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 16 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:04,503 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.020.04/ctd2.nc INFO 2025-06-26 10:31:04,504 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 10:31:04,505 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 10:31:04,505 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:31:04,521 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:31:05,121 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [58200] INFO 2025-06-26 10:31:05,231 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:31:05,237 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 10:31:05,237 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.020.04 ERROR 2025-06-26 10:31:05,237 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.020.04 INFO 2025-06-26 10:31:05,289 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_cal.nc INFO 2025-06-26 10:31:05,363 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 10:31:05,367 process.py align():251 [1] Alignment steps for 2005.020.04 INFO 2025-06-26 10:31:05,396 align.py process_cal():139 [1] Processing dorado_2005.020.04_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.020.04 INFO 2025-06-26 10:31:05,415 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:05,418 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:05,466 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:05,470 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:05,517 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:05,520 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:05,548 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:31:05,548 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:31:05,568 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:05,571 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:05,616 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:31:05,619 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,661 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:31:05,664 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,705 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:31:05,708 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,749 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:05,752 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,794 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:05,797 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,838 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:05,842 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,884 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:05,887 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,929 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:05,933 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:05,975 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:05,979 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,021 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,025 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,069 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,072 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,115 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,119 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,161 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,164 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,207 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,211 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,254 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,257 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,300 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,304 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,348 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,352 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,395 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,399 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,443 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,446 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,490 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.020.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:06,493 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:06,540 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:31:06,570 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:31:06,601 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:31:06,633 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:31:06,668 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:06,702 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_align.nc INFO 2025-06-26 10:31:06,767 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 10:31:06,769 process.py resample():273 [1] Resampling steps for 2005.020.04 INFO 2025-06-26 10:31:06,770 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:31:06,794 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_align.nc mission netCDF file INFO 2025-06-26 10:31:06,799 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_align.nc mission netCDF file INFO 2025-06-26 10:31:06,800 resample.py get_mission_start_end():1145 [1] navigation: 2005-01-20T18:07:30.613732992 to 2005-01-20T21:33:48.805768704 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:31:06,801 resample.py get_mission_start_end():1145 [1] hs2 : 2005-01-20T18:07:12.974941312 to 2005-01-20T21:33:48.635780352 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 10:31:06,803 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-01-20T18:07:36.553326080 to 2005-01-20T21:33:48.735773568 (0 days 00:00:00.069995136 before mission_end) INFO 2025-06-26 10:31:06,804 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-01-20T18:07:26.014048128 to 2005-01-20T21:33:48.715774976 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 10:31:06,806 resample.py get_mission_start_end():1145 [1] isus : 2005-01-20T18:08:33.229443584 to 2005-01-20T21:33:39.176428288 (0 days 00:00:09.629340416 before mission_end) INFO 2025-06-26 10:31:06,807 resample.py get_mission_start_end():1145 [1] biolume : 2005-01-20T18:07:08.165236480 to 2005-01-20T21:33:48.085783680 (0 days 00:00:00.719985024 before mission_end) INFO 2025-06-26 10:31:06,808 resample.py get_mission_start_end():1145 [1] tailcone : 2005-01-20T18:07:09.835156480 to 2005-01-20T21:33:48.805768704 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:31:06,809 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_align.nc mission netCDF file INFO 2025-06-26 10:31:06,809 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:06,958 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:06,986 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,013 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,041 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,067 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,091 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,115 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,139 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,161 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,183 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,205 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,227 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,248 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,270 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,293 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,316 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,342 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,367 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,390 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,413 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,437 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,460 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,471 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,481 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,490 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,503 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,529 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:07,695 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_1S.nc INFO 2025-06-26 10:31:08,668 create_products.py gulper_odv():401 [1] No gulper times found for 2005.020.04 INFO 2025-06-26 10:31:08,669 process.py archive():337 [1] Archiving steps for 2005.020.04 INFO 2025-06-26 10:31:08,669 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04, BASE_PATH = /data/auv_data INFO 2025-06-26 10:31:08,669 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:31:08,670 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.020.04_1S.nc INFO 2025-06-26 10:31:08,684 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:31:08,685 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.020.04_cal.nc INFO 2025-06-26 10:31:08,741 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:31:08,742 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.020.04_align.nc INFO 2025-06-26 10:31:08,796 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:31:08,818 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,834 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,841 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,853 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,902 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,909 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,923 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,937 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,973 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005020/2005.020.04 done. INFO 2025-06-26 10:31:08,973 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:31:08,973 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.020.04/dorado_2005.020.04_processing.log /Volumes/AUVCTD/surveys/2005/netcdf