INFO 2025-10-20 22:11:49,157 process.py process_mission():429 [1] commandline = /src/data/process_i2map.py -v --noinput --start_year 2018 --end_year 2018 --start_yd 1 --end_yd 365 --num_cores 1 --clobber
INFO 2025-10-20 22:11:49,157 process.py process_mission():449 [1] Processing i2map mission 2018.199.00 by user docker_user on host 6ad284762e9a
INFO 2025-10-20 22:11:49,157 process.py download_process():165 [1] Download and processing steps for 2018.199.00
INFO 2025-10-20 22:11:49,157 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/M3/master/i2MAP/2018/07/20180718/2018.199.00
INFO 2025-10-20 22:11:49,158 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/M3/master/i2MAP/2018/07/20180718/2018.199.00 to /data/auv_data/i2map/missionlogs/2018.199.00
INFO 2025-10-20 22:11:49,555 logs2netcdfs.py download_process_logs():779 [1] Processing mission: i2map 2018.199.00
INFO 2025-10-20 22:11:49,555 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2018.199.00/gps.log (784508 bytes)
INFO 2025-10-20 22:11:49,642 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2018.199.00/navigation.log (34650584 bytes)
INFO 2025-10-20 22:11:52,131 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2018.199.00/parosci.log (9753542 bytes)
INFO 2025-10-20 22:11:52,933 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2018.199.00/seabird25p.log (2942650 bytes)
INFO 2025-10-20 22:11:53,143 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/i2map/missionlogs/2018.199.00/seabird25p.log: [1]
INFO 2025-10-20 22:11:53,154 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/i2map/missionlogs/2018.199.00/tailCone.log (4882955 bytes)
WARNING 2025-10-20 22:11:53,575 logs2netcdfs.py _create_variable():536 [1] rudderCurrent: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,576 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of rudderCurrent.shape[0] (101718)
WARNING 2025-10-20 22:11:53,576 logs2netcdfs.py _create_variable():544 [1] rudderCurrent data is short by one, appending the last value: 0
WARNING 2025-10-20 22:11:53,585 logs2netcdfs.py _create_variable():536 [1] propCurrent1: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,585 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of propCurrent1.shape[0] (101718)
WARNING 2025-10-20 22:11:53,585 logs2netcdfs.py _create_variable():544 [1] propCurrent1 data is short by one, appending the last value: 0.3850601613521576
WARNING 2025-10-20 22:11:53,593 logs2netcdfs.py _create_variable():536 [1] propCurrent2: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,593 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of propCurrent2.shape[0] (101718)
WARNING 2025-10-20 22:11:53,593 logs2netcdfs.py _create_variable():544 [1] propCurrent2 data is short by one, appending the last value: 0
WARNING 2025-10-20 22:11:53,600 logs2netcdfs.py _create_variable():536 [1] propRpm: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,600 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of propRpm.shape[0] (101718)
WARNING 2025-10-20 22:11:53,600 logs2netcdfs.py _create_variable():544 [1] propRpm data is short by one, appending the last value: 0
WARNING 2025-10-20 22:11:53,608 logs2netcdfs.py _create_variable():536 [1] elevatorAngle: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,608 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of elevatorAngle.shape[0] (101718)
WARNING 2025-10-20 22:11:53,608 logs2netcdfs.py _create_variable():544 [1] elevatorAngle data is short by one, appending the last value: -0.07791522145271301
WARNING 2025-10-20 22:11:53,616 logs2netcdfs.py _create_variable():536 [1] rudderAngle: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,616 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of rudderAngle.shape[0] (101718)
WARNING 2025-10-20 22:11:53,616 logs2netcdfs.py _create_variable():544 [1] rudderAngle data is short by one, appending the last value: -0.18415972590446472
WARNING 2025-10-20 22:11:53,623 logs2netcdfs.py _create_variable():536 [1] propPwm: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,623 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of propPwm.shape[0] (101718)
WARNING 2025-10-20 22:11:53,623 logs2netcdfs.py _create_variable():544 [1] propPwm data is short by one, appending the last value: 0
WARNING 2025-10-20 22:11:53,630 logs2netcdfs.py _create_variable():536 [1] propTemp: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (101718,) and arg 1 with shape (101717,).
INFO 2025-10-20 22:11:53,630 logs2netcdfs.py _create_variable():537 [1] len(data) (101717) does not match shape of propTemp.shape[0] (101718)
WARNING 2025-10-20 22:11:53,630 logs2netcdfs.py _create_variable():544 [1] propTemp data is short by one, appending the last value: 0
INFO 2025-10-20 22:11:53,759 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.20 seconds
INFO 2025-10-20 22:11:53,759 process.py calibrate():227 [1] Calibration steps for 2018.199.00
INFO 2025-10-20 22:11:53,912 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 2025-10-20 22:11:53,913 calibrate.py _nudge_pos():1711 [1]                   -            -            -         0      0.00              -              -                             -
INFO 2025-10-20 22:11:54,576 calibrate.py _nudge_pos():1806 [1]   102:        0.050    0.0037883    0.0036669     47549    158.49          3.551          4.287 2018-07-18T18:44:41.089986816
INFO 2025-10-20 22:12:12,300 calibrate.py _nudge_pos():1806 [1]  1972:        0.190    0.0000645   -0.0000483        15      0.05        205.475       -191.931 2018-07-18T19:15:54.091677440
INFO 2025-10-20 22:12:46,674 calibrate.py _nudge_pos():1806 [1]  5573:        0.030   -0.0000013    0.0000155        20      0.06         -3.009         45.253 2018-07-18T20:16:05.494279424
INFO 2025-10-20 22:12:55,243 calibrate.py _nudge_pos():1806 [1]  6460:        0.100   -0.0000387   -0.0000017        35      0.11        -50.754         -2.723 2018-07-18T20:30:59.493036288
INFO 2025-10-20 22:13:32,881 calibrate.py _nudge_pos():1806 [1] 10359:        0.170    0.0000139   -0.0000003        15      0.05         44.232         -1.190 2018-07-18T21:36:05.695443200
INFO 2025-10-20 22:13:37,946 calibrate.py _nudge_pos():1862 [1] 10844:            -            -            -         3      0.01              -              -
INFO 2025-10-20 22:13:37,946 calibrate.py _nudge_pos():1868 [1] Points in final series = 101332
INFO 2025-10-20 22:13:39,539 calibrate.py _read_oxy_coeffs():1189 [1] Looking for calibration file for O2 sensor serial number 2935 on port side
INFO 2025-10-20 22:13:39,540 calibrate.py _read_oxy_coeffs():1219 [1] Executing: find "/Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files" -name "2935" 
INFO 2025-10-20 22:13:39,750 calibrate.py _read_oxy_coeffs():1238 [1] Found calibration date dirs: 2014_Nov 2021_Mar 2022_Apr
WARNING 2025-10-20 22:13:39,754 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2014_Nov
INFO 2025-10-20 22:13:39,754 calibrate.py _cal_date_xml_files():1087 [1] {xml_files}
WARNING 2025-10-20 22:13:39,758 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2021_Mar
INFO 2025-10-20 22:13:39,758 calibrate.py _cal_date_xml_files():1087 [1] {xml_files}
WARNING 2025-10-20 22:13:39,763 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr
INFO 2025-10-20 22:13:39,763 calibrate.py _cal_date_xml_files():1087 [1] {xml_files}
INFO 2025-10-20 22:13:39,769 calibrate.py _read_oxy_coeffs():1247 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml has CalibrationDate 2022-03-22 00:00:00+00:00
INFO 2025-10-20 22:13:39,769 calibrate.py _read_oxy_coeffs():1253 [1] Breaking from loop as /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml is after 2018.199.00 with mission_start=2018-07-18T16:04:44.517397248
INFO 2025-10-20 22:13:39,769 calibrate.py _read_oxy_coeffs():1270 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml is the first calibration file, but is after 2018.199.00 with mission_start=2018-07-18T16:04:44.517397248
INFO 2025-10-20 22:13:40,226 calibrate.py _calibrated_oxygen():2513 [1] dissolvedO2_port: parsed from /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/2935/2022_Apr/Oxygen_SBE43_2935.xml file: {'Soc': 0.42595, 'offset': -0.5339, 'A': -0.0041113, 'B': 0.00020802, 'C': -3.0027e-06, 'D0': 2.5826, 'D1': 0.000192634, 'D2': -0.0464803, 'E': 0.036, 'Tau20': 1.09, 'H1': -0.033, 'H2': 5000.0, 'H3': 1450.0}
INFO 2025-10-20 22:13:40,231 calibrate.py _read_oxy_coeffs():1189 [1] Looking for calibration file for O2 sensor serial number 3488 on stbd side
INFO 2025-10-20 22:13:40,231 calibrate.py _read_oxy_coeffs():1219 [1] Executing: find "/Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files" -name "3488" 
INFO 2025-10-20 22:13:40,411 calibrate.py _read_oxy_coeffs():1238 [1] Found calibration date dirs: 2016_dec 2021_mar 2022_Jan
WARNING 2025-10-20 22:13:40,415 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec
INFO 2025-10-20 22:13:40,415 calibrate.py _cal_date_xml_files():1087 [1] {xml_files}
WARNING 2025-10-20 22:13:40,420 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2021_mar
INFO 2025-10-20 22:13:40,420 calibrate.py _cal_date_xml_files():1087 [1] {xml_files}
WARNING 2025-10-20 22:13:40,424 calibrate.py _cal_date_xml_files():1081 [1] Found 4 xml files in /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2022_Jan
INFO 2025-10-20 22:13:40,424 calibrate.py _cal_date_xml_files():1087 [1] {xml_files}
INFO 2025-10-20 22:13:40,430 calibrate.py _read_oxy_coeffs():1247 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml has CalibrationDate 2016-12-16 00:00:00+00:00
INFO 2025-10-20 22:13:40,430 calibrate.py _read_oxy_coeffs():1263 [1] File /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml is just before 2018.199.00 with mission_start=2018-07-18T16:04:44.517397248
INFO 2025-10-20 22:13:40,892 calibrate.py _calibrated_oxygen():2513 [1] dissolvedO2_stbd: parsed from /Volumes/DMO/MDUC_CORE_CTD_200103/Calibration Files/SBE-43/3488/2016_dec/43-3488.xml file: {'Soc': 0.44664, 'offset': -0.507, 'A': -0.0030812, 'B': 7.8442e-05, 'C': -9.0601e-07, 'D0': 2.5826, 'D1': 0.000192634, 'D2': -0.0464803, 'E': 0.036, 'Tau20': 1.44, 'H1': -0.033, 'H2': 5000.0, 'H3': 1450.0}
INFO 2025-10-20 22:13:41,528 calibrate.py _geometric_depth_correction():3423 [1] seabird25p: d_beg_time_diff: 10 seconds, d_end_time_diff: -17341 seconds
INFO 2025-10-20 22:13:41,722 calibrate.py _geometric_depth_correction():3423 [1] seabird25p: d_beg_time_diff: 10 seconds, d_end_time_diff: -17341 seconds
INFO 2025-10-20 22:13:41,724 calibrate.py _ctd_process():2919 [1] Performing range checking of ['seabird25p_salinity'] in 2018.199.00/seabird25p.nc
INFO 2025-10-20 22:13:41,725 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 seabird25p_salinity values to NaN
INFO 2025-10-20 22:13:41,726 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('seabird25p_salinity', Range(min=30, max=40))]
INFO 2025-10-20 22:13:41,726 calibrate.py _range_qc_combined_nc():936 [1] Done range checking seabird25p
INFO 2025-10-20 22:13:41,805 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_cal.nc
INFO 2025-10-20 22:13:43,605 calibrate.py write_netcdf():3512 [1] Data variables written: depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_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, seabird25p_beam_transmittance, seabird25p_conductivity, seabird25p_conductivity_onboard, seabird25p_depth, seabird25p_dissolvedO2_port, seabird25p_dissolvedO2_stbd, seabird25p_oxygen_mll_port, seabird25p_oxygen_mll_stbd, seabird25p_oxygen_umolkg_port, seabird25p_oxygen_umolkg_stbd, seabird25p_salinity, seabird25p_salinity_onboard, seabird25p_temperature, seabird25p_temperature_onboard, seabird25p_time, tailcone_propRpm, tailcone_time, time
INFO 2025-10-20 22:13:43,608 process.py align():251 [1] Alignment steps for 2018.199.00
INFO 2025-10-20 22:13:43,631 align.py process_cal():139 [1] Processing i2map_2018.199.00_cal.nc from /data/auv_data/i2map/missionnetcdfs/2018.199.00
INFO 2025-10-20 22:13:43,659 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-10-20 22:13:43,663 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00
INFO 2025-10-20 22:13:43,736 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-10-20 22:13:43,743 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00
INFO 2025-10-20 22:13:43,812 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-10-20 22:13:43,816 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00
INFO 2025-10-20 22:13:43,857 align.py process_cal():161 [1] Skipping navigation_posx
INFO 2025-10-20 22:13:43,858 align.py process_cal():161 [1] Skipping navigation_posy
INFO 2025-10-20 22:13:43,886 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-10-20 22:13:43,891 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00
INFO 2025-10-20 22:13:43,953 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:43,956 align.py process_cal():249 [1] seabird25p_temperature: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:43,990 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:43,993 align.py process_cal():249 [1] seabird25p_conductivity: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,027 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,030 align.py process_cal():249 [1] seabird25p_salinity: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,064 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,067 align.py process_cal():249 [1] seabird25p_temperature_onboard: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,101 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,104 align.py process_cal():249 [1] seabird25p_conductivity_onboard: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,138 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,141 align.py process_cal():249 [1] seabird25p_salinity_onboard: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,176 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,179 align.py process_cal():249 [1] seabird25p_dissolvedO2_port: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,214 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,216 align.py process_cal():249 [1] seabird25p_oxygen_mll_port: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,251 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,254 align.py process_cal():249 [1] seabird25p_oxygen_umolkg_port: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,289 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,291 align.py process_cal():249 [1] seabird25p_dissolvedO2_stbd: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,326 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,329 align.py process_cal():249 [1] seabird25p_oxygen_mll_stbd: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,363 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,366 align.py process_cal():249 [1] seabird25p_oxygen_umolkg_stbd: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,401 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,403 align.py process_cal():249 [1] seabird25p_beam_transmittance: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,438 align.py process_cal():206 [1] Using pitch corrected seabird25p_depth: Variable depth_filtdepth from i2map_2018.199.00_cal.nc linearly interpolated to seabird25p_time and corrected for pitch using SensorOffset(x=4.04, y=0.0)
INFO 2025-10-20 22:13:44,440 align.py process_cal():249 [1] seabird25p_depth: instrument_sample_rate_hz = 7.99
INFO 2025-10-20 22:13:44,494 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00
INFO 2025-10-20 22:13:44,542 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_align.nc
INFO 2025-10-20 22:13:44,581 align.py write_netcdf():342 [1] Data variables written: navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, seabird25p_beam_transmittance, seabird25p_conductivity, seabird25p_conductivity_onboard, seabird25p_depth, seabird25p_dissolvedO2_port, seabird25p_dissolvedO2_stbd, seabird25p_latitude, seabird25p_longitude, seabird25p_oxygen_mll_port, seabird25p_oxygen_mll_stbd, seabird25p_oxygen_umolkg_port, seabird25p_oxygen_umolkg_stbd, seabird25p_salinity, seabird25p_salinity_onboard, seabird25p_temperature, seabird25p_temperature_onboard, seabird25p_time, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time
INFO 2025-10-20 22:13:44,583 process.py resample():273 [1] Resampling steps for 2018.199.00
INFO 2025-10-20 22:13:44,583 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m
INFO 2025-10-20 22:13:44,598 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_align.nc mission netCDF file
INFO 2025-10-20 22:13:44,601 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_align.nc mission netCDF file
INFO 2025-10-20 22:13:44,602 resample.py get_mission_start_end():1145 [1] navigation: 2018-07-18T16:05:10.725601792 to 2018-07-18T21:44:51.489423872 (0 days 00:00:00 before mission_end)
INFO 2025-10-20 22:13:44,604 resample.py get_mission_start_end():1145 [1] seabird25p: 2018-07-18T16:04:44.517397248 to 2018-07-18T16:55:50.777344000 (0 days 04:49:00.712079872 before mission_end)
WARNING 2025-10-20 22:13:44,604 resample.py get_mission_start_end():1156 [1] Instrument seabird25p has a gap > 5 minutes at the end of the mission: 0 days 04:49:00.712079872
INFO 2025-10-20 22:13:44,606 resample.py get_mission_start_end():1145 [1] tailcone  : 2018-07-18T16:04:42.647525120 to 2018-07-18T21:43:46.033907712 (0 days 00:01:05.455516160 before mission_end)
INFO 2025-10-20 22:13:44,607 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_align.nc mission netCDF file
INFO 2025-10-20 22:13:44,607 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter 
INFO 2025-10-20 22:13:44,839 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:44,873 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:44,907 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:44,939 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:44,957 resample.py resample_variable():1031 [1] Resampling seabird25p_temperature with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:44,957 resample.py resample_variable():1038 [1] Padding seabird25p_temperature with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:44,974 resample.py resample_variable():1031 [1] Resampling seabird25p_conductivity with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:44,974 resample.py resample_variable():1038 [1] Padding seabird25p_conductivity with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:44,989 resample.py resample_variable():1031 [1] Resampling seabird25p_salinity with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:44,989 resample.py resample_variable():1038 [1] Padding seabird25p_salinity with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,005 resample.py resample_variable():1031 [1] Resampling seabird25p_temperature_onboard with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,005 resample.py resample_variable():1038 [1] Padding seabird25p_temperature_onboard with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,021 resample.py resample_variable():1031 [1] Resampling seabird25p_conductivity_onboard with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,021 resample.py resample_variable():1038 [1] Padding seabird25p_conductivity_onboard with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,037 resample.py resample_variable():1031 [1] Resampling seabird25p_salinity_onboard with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,037 resample.py resample_variable():1038 [1] Padding seabird25p_salinity_onboard with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,052 resample.py resample_variable():1031 [1] Resampling seabird25p_dissolvedO2_port with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,053 resample.py resample_variable():1038 [1] Padding seabird25p_dissolvedO2_port with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,068 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_mll_port with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,068 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_mll_port with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,084 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_umolkg_port with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,084 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_umolkg_port with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,100 resample.py resample_variable():1031 [1] Resampling seabird25p_dissolvedO2_stbd with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,100 resample.py resample_variable():1038 [1] Padding seabird25p_dissolvedO2_stbd with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,116 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_mll_stbd with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,116 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_mll_stbd with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,132 resample.py resample_variable():1031 [1] Resampling seabird25p_oxygen_umolkg_stbd with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,133 resample.py resample_variable():1038 [1] Padding seabird25p_oxygen_umolkg_stbd with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,149 resample.py resample_variable():1031 [1] Resampling seabird25p_beam_transmittance with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,149 resample.py resample_variable():1038 [1] Padding seabird25p_beam_transmittance with 0 days 04:49:00.712079872 of NaNs to the end of mission
INFO 2025-10-20 22:13:45,184 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter
INFO 2025-10-20 22:13:45,364 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_1S.nc
INFO 2025-10-20 22:13:45,365 process.py archive():337 [1] Archiving steps for 2018.199.00
INFO 2025-10-20 22:13:45,366 process.py archive():347 [1] nc_file_base = /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00, BASE_PATH = /data/auv_data
INFO 2025-10-20 22:13:45,367 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00 files to /Volumes/AUVCTD/surveys/2018/netcdf
INFO 2025-10-20 22:13:45,368 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2018/netcdf/i2map_2018.199.00_1S.nc
INFO 2025-10-20 22:13:45,386 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_1S.nc /Volumes/AUVCTD/surveys/2018/netcdf done.
INFO 2025-10-20 22:13:45,387 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2018/netcdf/i2map_2018.199.00_cal.nc
INFO 2025-10-20 22:13:45,439 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_cal.nc /Volumes/AUVCTD/surveys/2018/netcdf done.
INFO 2025-10-20 22:13:45,440 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2018/netcdf/i2map_2018.199.00_align.nc
INFO 2025-10-20 22:13:45,476 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_align.nc /Volumes/AUVCTD/surveys/2018/netcdf done.
INFO 2025-10-20 22:13:45,487 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2018/2018199/2018.199.00 done.
INFO 2025-10-20 22:13:45,573 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2018/2018199/2018.199.00 done.
INFO 2025-10-20 22:13:45,602 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2018/2018199/2018.199.00 done.
INFO 2025-10-20 22:13:45,614 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/seabird25p.nc /Volumes/AUVCTD/missionnetcdfs/2018/2018199/2018.199.00 done.
INFO 2025-10-20 22:13:45,632 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2018/2018199/2018.199.00 done.
INFO 2025-10-20 22:13:45,632 archive.py copy_to_AUVTCD():116 [1] Archiving product files
INFO 2025-10-20 22:13:45,633 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/i2map/missionnetcdfs/2018.199.00/i2map_2018.199.00_processing.log /Volumes/AUVCTD/surveys/2018/netcdf