INFO 2025-06-26 19:00:26,873 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 19:00:26,874 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX missions - Initial engineering test from Yanwu & Frederic - ctdToUse = ctd1 INFO 2025-06-26 19:00:26,874 process.py process_mission():449 [1] Processing AUVCTD mission 2012.142.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:00:26,874 process.py download_process():165 [1] Download and processing steps for 2012.142.02 INFO 2025-06-26 19:00:26,874 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012142/2012.142.02 INFO 2025-06-26 19:00:26,874 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012142/2012.142.02 to /data/auv_data/dorado/missionlogs/2012.142.02 INFO 2025-06-26 19:00:28,240 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.142.02 INFO 2025-06-26 19:00:28,241 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/ctdDriver.log (782886 bytes) INFO 2025-06-26 19:00:28,333 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/ctdDriver2.log (783071 bytes) INFO 2025-06-26 19:00:28,411 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/gps.log (36140 bytes) INFO 2025-06-26 19:00:28,424 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/hydroscatlog.log (692686 bytes) INFO 2025-06-26 19:00:28,523 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/navigation.log (2760118 bytes) INFO 2025-06-26 19:00:28,772 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/parosci.log (833990 bytes) INFO 2025-06-26 19:00:28,873 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/tailCone.log (496075 bytes) INFO 2025-06-26 19:00:28,950 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/biolume.log (580066 bytes) INFO 2025-06-26 19:00:29,027 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:00:29,077 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.84 seconds INFO 2025-06-26 19:00:29,078 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.02/lopc.bin (7066000 bytes) INFO 2025-06-26 19:00:29,078 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:00:29 2025 INFO 2025-06-26 19:00:29,079 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2012.142.02/parosci.nc INFO 2025-06-26 19:00:29,079 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:00:29,079 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2012.142.02/parosci.nc INFO 2025-06-26 19:00:29,081 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1337634108.7, sensor_off_time = 1337636173.8 INFO 2025-06-26 19:00:29,081 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 2065 seconds. Expecting to read 4130 L frames from the lopc.bin file. INFO 2025-06-26 19:00:29,081 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 4130 records from the lopc.bin file. INFO 2025-06-26 19:00:29,112 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2012-05-21 21:01:48 Z and endTime = 2012-05-21 21:36:13 Z with 4130 records expected to be read from lopc.bin INFO 2025-06-26 19:00:29,112 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2012.142.02/lopc.bin INFO 2025-06-26 19:00:29,112 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2012.142.02/lopc.nc INFO 2025-06-26 19:00:29,113 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2012.142.02/lopc.nc INFO 2025-06-26 19:00:29,114 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2012.142.02 INFO 2025-06-26 19:00:29,114 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:00:29,122 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0198192 WARNING 2025-06-26 19:00:29,122 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = ERROR 2025-06-26 19:00:29,131 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:00:29,132 process.py calibrate():227 [1] Calibration steps for 2012.142.02 INFO 2025-06-26 19:00:29,240 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 19:00:29,242 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:00:30,278 calibrate.py _nudge_pos():1806 [1] 132: 0.180 -0.0009033 -0.0036320 7880 26.26 -5.098 -25.625 2012-05-21T21:30:16.012534016 INFO 2025-06-26 19:00:33,880 calibrate.py _nudge_pos():1862 [1] 452: - - - 4 0.01 - - INFO 2025-06-26 19:00:33,880 calibrate.py _nudge_pos():1868 [1] Points in final series = 10139 WARNING 2025-06-26 19:00:33,898 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:00:33,991 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:00:34,092 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:34,156 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:34,158 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.142.02/ctd1.nc INFO 2025-06-26 19:00:34,159 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:00:34,159 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 19:00:34,159 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:00:34,246 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:34,312 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:34,313 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.142.02/ctd2.nc INFO 2025-06-26 19:00:34,315 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:00:34,315 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 19:00:34,315 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:00:34,316 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.142.02 INFO 2025-06-26 19:00:34,319 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:00:34,429 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:00:34,442 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2012.142.02 ERROR 2025-06-26 19:00:34,443 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.142.02 INFO 2025-06-26 19:00:34,455 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_cal.nc INFO 2025-06-26 19:00:34,509 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_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 19:00:34,516 process.py align():251 [1] Alignment steps for 2012.142.02 INFO 2025-06-26 19:00:34,547 align.py process_cal():139 [1] Processing dorado_2012.142.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.142.02 INFO 2025-06-26 19:00:34,556 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:34,558 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:34,577 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:34,579 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:34,595 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:34,597 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:34,606 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:00:34,606 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:00:34,612 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:34,614 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:34,629 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,631 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,646 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,648 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,682 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,685 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,700 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,702 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,716 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,719 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,732 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,735 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,749 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,751 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,766 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,768 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,784 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,787 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,802 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,804 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,819 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,822 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,837 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,840 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,855 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,858 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,875 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,877 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,895 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,899 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,917 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,920 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,936 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,939 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,957 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,960 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,977 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,980 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:34,996 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:34,999 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:35,017 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:35,020 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:35,039 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:35,042 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:35,064 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:00:35,085 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:00:35,111 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 19:00:35,198 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:35,215 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_align.nc INFO 2025-06-26 19:00:35,287 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_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 19:00:35,290 process.py resample():273 [1] Resampling steps for 2012.142.02 INFO 2025-06-26 19:00:35,291 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:00:35,319 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_align.nc mission netCDF file INFO 2025-06-26 19:00:35,323 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_align.nc mission netCDF file INFO 2025-06-26 19:00:35,324 resample.py get_mission_start_end():1145 [1] navigation: 2012-05-21T21:02:26.226921984 to 2012-05-21T21:36:13.808023296 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 19:00:35,325 resample.py get_mission_start_end():1145 [1] hs2 : 2012-05-21T21:01:54.519094272 to 2012-05-21T21:36:13.818022400 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 19:00:35,327 resample.py get_mission_start_end():1145 [1] ctd1 : 2012-05-21T21:02:16.577583104 to 2012-05-21T21:36:13.758026496 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 19:00:35,328 resample.py get_mission_start_end():1145 [1] ctd2 : 2012-05-21T21:02:16.597581824 to 2012-05-21T21:36:13.758026496 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 19:00:35,330 resample.py get_mission_start_end():1145 [1] biolume : 2012-05-21T21:01:47.669529088 to 2012-05-21T21:36:13.208030208 (0 days 00:00:00.639990272 before mission_end) INFO 2025-06-26 19:00:35,331 resample.py get_mission_start_end():1145 [1] tailcone : 2012-05-21T21:01:49.249455104 to 2012-05-21T21:36:13.848020480 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:00:35,331 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_align.nc mission netCDF file INFO 2025-06-26 19:00:35,332 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,386 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,399 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,412 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,424 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,436 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,448 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,460 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,471 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,482 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,492 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,502 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,512 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,522 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,532 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,543 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,552 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,563 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,575 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,585 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,597 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,610 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,623 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,638 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,666 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,675 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,684 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,689 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:00:35,689 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:00:35,765 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:00:35,784 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:00:35,795 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:00:35,800 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:00:35,807 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:00:35,808 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:00:35,825 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:35,941 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_1S.nc INFO 2025-06-26 19:00:37,542 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:00:37,726 create_products.py gulper_odv():522 [1] Wrote 1 Gulper data lines to /data/auv_data/dorado/missionodvs/2012.142.02/dorado_2012.142.02_1S_Gulper.txt INFO 2025-06-26 19:00:37,726 process.py archive():337 [1] Archiving steps for 2012.142.02 INFO 2025-06-26 19:00:37,726 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02, BASE_PATH = /data/auv_data INFO 2025-06-26 19:00:37,726 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02 files to /Volumes/AUVCTD/surveys/2012/netcdf INFO 2025-06-26 19:00:37,727 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.142.02_1S.nc INFO 2025-06-26 19:00:37,735 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:37,736 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.142.02_cal.nc INFO 2025-06-26 19:00:37,757 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:37,758 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.142.02_align.nc INFO 2025-06-26 19:00:37,789 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:37,798 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,805 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,810 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,819 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,832 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,842 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,852 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,866 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,872 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.02 done. INFO 2025-06-26 19:00:37,872 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:00:37,873 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2012/odv/dorado_2012.142.02_1S_Gulper.txt INFO 2025-06-26 19:00:37,879 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2012.142.02/dorado_2012.142.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2012/odv done. INFO 2025-06-26 19:00:37,879 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.02/dorado_2012.142.02_processing.log /Volumes/AUVCTD/surveys/2012/netcdf