INFO 2025-06-26 10:31:34,742 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 10:31:34,742 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Elkhorn Slough plume racetrack Monterey triangle - ctdToUse = ctd1 INFO 2025-06-26 10:31:34,742 process.py process_mission():449 [1] Processing OCCO mission 2005.021.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:31:34,742 process.py download_process():165 [1] Download and processing steps for 2005.021.01 INFO 2025-06-26 10:31:34,742 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005021/2005.021.01 INFO 2025-06-26 10:31:34,743 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005021/2005.021.01 to /data/auv_data/dorado/missionlogs/2005.021.01 INFO 2025-06-26 10:31:34,889 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.021.01 INFO 2025-06-26 10:31:34,889 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/ctdDriver.log (777875 bytes) INFO 2025-06-26 10:31:34,952 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/ctdDriver2.log (781565 bytes) INFO 2025-06-26 10:31:35,015 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/gps.log (21956 bytes) INFO 2025-06-26 10:31:35,025 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/hydroscatlog.log (536174 bytes) INFO 2025-06-26 10:31:35,094 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/navigation.log (2616422 bytes) INFO 2025-06-26 10:31:35,291 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/isuslog.log (9173 bytes) INFO 2025-06-26 10:31:35,296 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/parosci.log (525734 bytes) INFO 2025-06-26 10:31:35,342 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/tailCone.log (537211 bytes) INFO 2025-06-26 10:31:35,413 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.021.01/biolume.log (611324 bytes) INFO 2025-06-26 10:31:35,474 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:31:35,510 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.62 seconds WARNING 2025-06-26 10:31:35,511 process.py download_process():196 [1] No lopc.bin file for 2005.021.01 INFO 2025-06-26 10:31:35,511 process.py calibrate():227 [1] Calibration steps for 2005.021.01 INFO 2025-06-26 10:31:35,580 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 10:31:35,582 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:31:36,422 calibrate.py _nudge_pos():1806 [1] 107: 0.160 0.0000111 -0.0000115 55 0.18 9.181 -11.836 2005-01-21T18:04:13.951443968 INFO 2025-06-26 10:31:36,460 calibrate.py _nudge_pos():1806 [1] 111: 0.150 -0.0000221 -0.0001141 3250 10.83 -0.303 -1.953 2005-01-21T18:15:06.956710144 INFO 2025-06-26 10:31:37,184 calibrate.py _nudge_pos():1806 [1] 189: 0.150 -0.0011846 -0.0007798 5705 19.01 -9.244 -7.599 2005-01-21T18:35:24.953271680 INFO 2025-06-26 10:31:37,617 calibrate.py _nudge_pos():1806 [1] 236: 0.160 -0.0001363 -0.0000620 730 2.43 -8.322 -4.732 2005-01-21T18:38:36.950118784 INFO 2025-06-26 10:31:38,144 calibrate.py _nudge_pos():1862 [1] 272: - - - 3 0.01 - - INFO 2025-06-26 10:31:38,144 calibrate.py _nudge_pos():1868 [1] Points in final series = 11078 WARNING 2025-06-26 10:31:38,157 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 10:31:38,253 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:31:38,355 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:38,424 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:38,425 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.021.01/ctd1.nc INFO 2025-06-26 10:31:38,426 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 10:31:38,427 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 10:31:38,427 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:31:38,518 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:38,586 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:31:38,588 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.021.01/ctd2.nc INFO 2025-06-26 10:31:38,589 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 10:31:38,590 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 10:31:38,590 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:31:38,598 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:31:38,717 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:31:38,722 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 10:31:38,722 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.021.01 ERROR 2025-06-26 10:31:38,722 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.021.01 INFO 2025-06-26 10:31:38,734 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_cal.nc INFO 2025-06-26 10:31:38,780 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 10:31:38,784 process.py align():251 [1] Alignment steps for 2005.021.01 INFO 2025-06-26 10:31:38,806 align.py process_cal():139 [1] Processing dorado_2005.021.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.021.01 INFO 2025-06-26 10:31:38,813 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:38,815 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:38,831 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:38,833 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:38,847 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:38,849 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:38,858 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:31:38,858 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:31:38,864 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:31:38,866 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:38,880 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:31:38,882 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:38,897 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:31:38,898 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:38,912 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:31:38,914 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:38,928 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:38,930 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:38,944 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:38,946 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:38,960 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:38,962 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:38,977 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:38,979 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:38,994 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:38,996 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,012 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,014 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,028 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,030 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,045 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,047 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,061 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,063 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,078 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,079 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,094 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,096 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,112 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,114 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,129 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,131 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,146 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,148 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,163 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,165 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,181 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,183 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,198 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.021.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:31:39,200 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:31:39,217 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:31:39,232 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:31:39,246 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 10:31:39,263 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:31:39,280 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:31:39,295 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_align.nc INFO 2025-06-26 10:31:39,341 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 10:31:39,343 process.py resample():273 [1] Resampling steps for 2005.021.01 INFO 2025-06-26 10:31:39,343 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:31:39,366 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_align.nc mission netCDF file INFO 2025-06-26 10:31:39,370 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_align.nc mission netCDF file INFO 2025-06-26 10:31:39,371 resample.py get_mission_start_end():1145 [1] navigation: 2005-01-21T18:02:38.158006144 to 2005-01-21T18:39:33.556241024 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:31:39,373 resample.py get_mission_start_end():1145 [1] hs2 : 2005-01-21T18:02:22.429083776 to 2005-01-21T18:39:33.466247296 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 10:31:39,374 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-01-21T18:02:45.837480064 to 2005-01-21T18:39:33.526243200 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 10:31:39,376 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-01-21T18:02:35.328200064 to 2005-01-21T18:39:33.516243712 (0 days 00:00:00.039997312 before mission_end) INFO 2025-06-26 10:31:39,377 resample.py get_mission_start_end():1145 [1] isus : 2005-01-21T18:03:41.703653120 to 2005-01-21T18:39:29.436523136 (0 days 00:00:04.119717888 before mission_end) INFO 2025-06-26 10:31:39,378 resample.py get_mission_start_end():1145 [1] biolume : 2005-01-21T18:02:17.019420160 to 2005-01-21T18:39:32.816257536 (0 days 00:00:00.739983488 before mission_end) INFO 2025-06-26 10:31:39,379 resample.py get_mission_start_end():1145 [1] tailcone : 2005-01-21T18:02:16.989456384 to 2005-01-21T18:39:33.506244480 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 10:31:39,380 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_align.nc mission netCDF file INFO 2025-06-26 10:31:39,380 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,430 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,441 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,453 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,465 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,476 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,489 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,501 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,512 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,522 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,531 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,540 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,549 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,558 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,568 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,577 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,586 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,597 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,608 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,618 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,628 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,638 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,648 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,657 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,665 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,673 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,683 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,695 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:31:39,801 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_1S.nc INFO 2025-06-26 10:31:40,467 create_products.py gulper_odv():401 [1] No gulper times found for 2005.021.01 INFO 2025-06-26 10:31:40,467 process.py archive():337 [1] Archiving steps for 2005.021.01 INFO 2025-06-26 10:31:40,467 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01, BASE_PATH = /data/auv_data INFO 2025-06-26 10:31:40,467 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:31:40,469 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.021.01_1S.nc INFO 2025-06-26 10:31:40,477 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:31:40,478 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.021.01_cal.nc INFO 2025-06-26 10:31:40,492 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:31:40,493 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.021.01_align.nc INFO 2025-06-26 10:31:40,508 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:31:40,517 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,524 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,528 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,535 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,548 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,552 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,559 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,566 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,577 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005021/2005.021.01 done. INFO 2025-06-26 10:31:40,577 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:31:40,577 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.021.01/dorado_2005.021.01_processing.log /Volumes/AUVCTD/surveys/2005/netcdf