INFO 2025-06-26 19:00:52,303 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 19:00:52,303 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX missions - Initial engineering test from Yanwu & Frederic - ctdToUse = ctd1 
INFO 2025-06-26 19:00:52,303 process.py process_mission():449 [1] Processing AUVCTD mission 2012.143.08 by user docker_user on host eae60d30a712
INFO 2025-06-26 19:00:52,303 process.py download_process():165 [1] Download and processing steps for 2012.143.08
INFO 2025-06-26 19:00:52,304 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012143/2012.143.08
INFO 2025-06-26 19:00:52,304 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012143/2012.143.08 to /data/auv_data/dorado/missionlogs/2012.143.08
INFO 2025-06-26 19:00:53,494 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.143.08
INFO 2025-06-26 19:00:53,494 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/ctdDriver.log (1243494 bytes)
INFO 2025-06-26 19:00:53,591 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/ctdDriver2.log (1243775 bytes)
INFO 2025-06-26 19:00:53,705 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/gps.log (64436 bytes)
INFO 2025-06-26 19:00:53,721 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/hydroscatlog.log (1094710 bytes)
INFO 2025-06-26 19:00:53,850 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/navigation.log (4392934 bytes)
INFO 2025-06-26 19:00:54,203 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/parosci.log (1328486 bytes)
INFO 2025-06-26 19:00:54,337 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/tailCone.log (784123 bytes)
INFO 2025-06-26 19:00:54,443 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/biolume.log (915186 bytes)
INFO 2025-06-26 19:00:54,541 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data
INFO 2025-06-26 19:00:54,598 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.10 seconds
INFO 2025-06-26 19:00:54,599 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.08/lopc.bin (5052000 bytes)
INFO 2025-06-26 19:00:54,599 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:00:54 2025
INFO 2025-06-26 19:00:54,599 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2012.143.08/parosci.nc
INFO 2025-06-26 19:00:54,599 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL:
INFO 2025-06-26 19:00:54,599 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2012.143.08/parosci.nc
INFO 2025-06-26 19:00:54,601 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1337717373.5, sensor_off_time = 1337720639.2
INFO 2025-06-26 19:00:54,602 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 3265 seconds.  Expecting to read 6530 L frames from the lopc.bin file.
INFO 2025-06-26 19:00:54,602 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 6530 records from the lopc.bin file.
INFO 2025-06-26 19:00:54,641 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2012-05-22 20:09:33 Z and endTime = 2012-05-22 21:03:59 Z with 6530 records expected to be read from lopc.bin
INFO 2025-06-26 19:00:54,641 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2012.143.08/lopc.bin
INFO 2025-06-26 19:00:54,641 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2012.143.08/lopc.nc
INFO 2025-06-26 19:00:54,641 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2012.143.08/lopc.nc
INFO 2025-06-26 19:00:54,642 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2012.143.08
INFO 2025-06-26 19:00:54,642 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994
WARNING 2025-06-26 19:00:54,645 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A01414412
WARNING 2025-06-26 19:00:54,645 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = 
INFO 2025-06-26 19:00:54,729 lopcToNetCDF.py unpackLOPCbin():951 [1]   L Frames     sample     M Frames  ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L  
INFO 2025-06-26 19:00:54,729 lopcToNetCDF.py unpackLOPCbin():969 [1]    Count       Count       Count       Error       Error       Error       Error       Error    
INFO 2025-06-26 19:00:54,729 lopcToNetCDF.py unpackLOPCbin():987 [1]   --------    --------    --------  ----------- ----------- ----------- ----------- ------------
ERROR 2025-06-26 19:00:56,763 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt
INFO 2025-06-26 19:00:56,763 process.py calibrate():227 [1] Calibration steps for 2012.143.08
INFO 2025-06-26 19:00:56,862 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 19:00:56,864 calibrate.py _nudge_pos():1711 [1]                   -            -            -         0      0.00              -              -                             -
INFO 2025-06-26 19:00:58,013 calibrate.py _nudge_pos():1806 [1]   143:        0.170   -0.0009503   -0.0062808      5540     18.46         -7.634        -63.035 2012-05-22T20:30:22.329912576
INFO 2025-06-26 19:00:58,199 calibrate.py _nudge_pos():1806 [1]   162:        0.170   -0.0000150    0.0000378        25      0.08        -27.829         87.504 2012-05-22T20:30:46.328268544
INFO 2025-06-26 19:00:58,362 calibrate.py _nudge_pos():1806 [1]   179:        0.180    0.0000051   -0.0000048        15      0.05         16.203        -18.961 2012-05-22T20:31:05.326967296
INFO 2025-06-26 19:00:58,497 calibrate.py _nudge_pos():1806 [1]   193:        0.170    0.0000323   -0.0000086        15      0.05        102.832        -34.083 2012-05-22T20:31:21.325871104
INFO 2025-06-26 19:00:58,876 calibrate.py _nudge_pos():1806 [1]   231:        0.180   -0.0000208   -0.0000433        20      0.06        -48.737       -126.583 2012-05-22T20:32:02.323062784
INFO 2025-06-26 19:00:59,010 calibrate.py _nudge_pos():1806 [1]   244:        0.170   -0.0000010   -0.0000115        15      0.05         -3.319        -45.797 2012-05-22T20:32:17.332034304
INFO 2025-06-26 19:00:59,059 calibrate.py _nudge_pos():1806 [1]   249:        0.180   -0.0005823   -0.0045589      6275     20.91         -4.130        -40.394 2012-05-22T20:53:16.325787648
INFO 2025-06-26 19:00:59,080 calibrate.py _nudge_pos():1806 [1]   251:        0.180   -0.0000727   -0.0000097        35      0.11        -95.135        -15.815 2012-05-22T20:53:24.325239296
INFO 2025-06-26 19:01:03,552 calibrate.py _nudge_pos():1806 [1]   692:        0.170   -0.0000111   -0.0000353        15      0.05        -35.253       -140.102 2012-05-22T21:00:48.324823296
INFO 2025-06-26 19:01:05,446 calibrate.py _nudge_pos():1862 [1]  845:            -            -            -         4      0.01              -              -
INFO 2025-06-26 19:01:05,447 calibrate.py _nudge_pos():1868 [1] Points in final series = 16142
WARNING 2025-06-26 19:01:05,474 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz
INFO 2025-06-26 19:01:05,620 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds
INFO 2025-06-26 19:01:05,785 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds
INFO 2025-06-26 19:01:05,888 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds
INFO 2025-06-26 19:01:05,889 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.143.08/ctd1.nc
INFO 2025-06-26 19:01:05,890 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN
INFO 2025-06-26 19:01:05,891 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 19:01:05,891 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1
INFO 2025-06-26 19:01:06,040 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds
INFO 2025-06-26 19:01:06,143 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds
INFO 2025-06-26 19:01:06,145 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.143.08/ctd2.nc
INFO 2025-06-26 19:01:06,146 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN
INFO 2025-06-26 19:01:06,147 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 19:01:06,147 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2
ERROR 2025-06-26 19:01:06,147 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.143.08
INFO 2025-06-26 19:01:06,151 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz
INFO 2025-06-26 19:01:06,410 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63]
INFO 2025-06-26 19:01:06,442 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds
ERROR 2025-06-26 19:01:09,487 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2012.143.08
ERROR 2025-06-26 19:01:09,487 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.143.08
INFO 2025-06-26 19:01:09,505 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_cal.nc
INFO 2025-06-26 19:01:09,569 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 19:01:09,577 process.py align():251 [1] Alignment steps for 2012.143.08
INFO 2025-06-26 19:01:09,608 align.py process_cal():139 [1] Processing dorado_2012.143.08_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.143.08
INFO 2025-06-26 19:01:09,617 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 19:01:09,619 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 19:01:09,640 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 19:01:09,643 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 19:01:09,678 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 19:01:09,680 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 19:01:09,692 align.py process_cal():161 [1] Skipping navigation_posx
INFO 2025-06-26 19:01:09,692 align.py process_cal():161 [1] Skipping navigation_posy
INFO 2025-06-26 19:01:09,700 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 19:01:09,702 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 19:01:09,721 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,723 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,741 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,744 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,761 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,764 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,781 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,784 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,802 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,804 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,822 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,825 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,847 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,866 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,868 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,886 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,889 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,908 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,911 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,930 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,933 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,954 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,957 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,977 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:09,980 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:09,998 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,001 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,020 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,023 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,043 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,046 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,065 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,069 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,088 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,091 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,110 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,113 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,132 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,134 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,153 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,156 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,174 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2025-06-26 19:01:10,176 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 19:01:10,201 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98
INFO 2025-06-26 19:01:10,222 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98
INFO 2025-06-26 19:01:10,246 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99
INFO 2025-06-26 19:01:10,353 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 19:01:10,371 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_align.nc
INFO 2025-06-26 19:01:10,436 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 19:01:10,440 process.py resample():273 [1] Resampling steps for 2012.143.08
INFO 2025-06-26 19:01:10,440 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m
INFO 2025-06-26 19:01:10,467 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_align.nc mission netCDF file
INFO 2025-06-26 19:01:10,471 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_align.nc mission netCDF file
INFO 2025-06-26 19:01:10,472 resample.py get_mission_start_end():1145 [1] navigation: 2012-05-22T20:10:10.942898176 to 2012-05-22T21:03:59.161750016 (0 days 00:00:00.159989248 before mission_end)
INFO 2025-06-26 19:01:10,473 resample.py get_mission_start_end():1145 [1] hs2       : 2012-05-22T20:09:42.294860800 to 2012-05-22T21:03:59.161750016 (0 days 00:00:00.159989248 before mission_end)
INFO 2025-06-26 19:01:10,475 resample.py get_mission_start_end():1145 [1] ctd1      : 2012-05-22T20:10:01.883518976 to 2012-05-22T21:03:59.291741440 (0 days 00:00:00.029997824 before mission_end)
INFO 2025-06-26 19:01:10,476 resample.py get_mission_start_end():1145 [1] ctd2      : 2012-05-22T20:10:01.653534720 to 2012-05-22T21:03:59.311739904 (0 days 00:00:00.009999360 before mission_end)
INFO 2025-06-26 19:01:10,477 resample.py get_mission_start_end():1145 [1] biolume   : 2012-05-22T20:09:32.575492352 to 2012-05-22T21:03:58.361770752 (0 days 00:00:00.959968512 before mission_end)
INFO 2025-06-26 19:01:10,479 resample.py get_mission_start_end():1145 [1] tailcone  : 2012-05-22T20:09:34.535392512 to 2012-05-22T21:03:59.321739264 (0 days 00:00:00 before mission_end)
INFO 2025-06-26 19:01:10,479 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_align.nc mission netCDF file
INFO 2025-06-26 19:01:10,480 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter 
INFO 2025-06-26 19:01:10,544 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,559 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,573 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,587 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,601 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,615 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,630 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,643 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,669 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,682 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,693 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,705 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,717 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,729 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,741 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,753 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,765 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,780 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,794 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,808 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,821 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,834 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,847 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,860 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,869 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,877 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:10,881 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4
INFO 2025-06-26 19:01:10,881 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw
INFO 2025-06-26 19:01:10,987 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11
INFO 2025-06-26 19:01:11,012 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low
INFO 2025-06-26 19:01:11,026 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope
INFO 2025-06-26 19:01:11,033 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy)
INFO 2025-06-26 19:01:11,042 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission.
INFO 2025-06-26 19:01:11,042 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies
INFO 2025-06-26 19:01:11,061 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter
INFO 2025-06-26 19:01:11,190 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_1S.nc
INFO 2025-06-26 19:01:12,690 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1
INFO 2025-06-26 19:01:13,821 create_products.py gulper_odv():522 [1] Wrote 7 Gulper data lines to /data/auv_data/dorado/missionodvs/2012.143.08/dorado_2012.143.08_1S_Gulper.txt
INFO 2025-06-26 19:01:13,821 process.py archive():337 [1] Archiving steps for 2012.143.08
INFO 2025-06-26 19:01:13,821 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08, BASE_PATH = /data/auv_data
INFO 2025-06-26 19:01:13,821 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08 files to /Volumes/AUVCTD/surveys/2012/netcdf
INFO 2025-06-26 19:01:13,824 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.143.08_1S.nc
INFO 2025-06-26 19:01:13,835 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done.
INFO 2025-06-26 19:01:13,837 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.143.08_cal.nc
INFO 2025-06-26 19:01:13,866 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done.
INFO 2025-06-26 19:01:13,867 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.143.08_align.nc
INFO 2025-06-26 19:01:13,909 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done.
INFO 2025-06-26 19:01:13,920 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:13,929 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:13,934 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:13,945 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:13,962 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:13,973 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:13,982 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:13,997 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:14,009 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.08 done.
INFO 2025-06-26 19:01:14,010 archive.py copy_to_AUVTCD():116 [1] Archiving product files
INFO 2025-06-26 19:01:14,011 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2012/odv/dorado_2012.143.08_1S_Gulper.txt
INFO 2025-06-26 19:01:14,022 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2012.143.08/dorado_2012.143.08_1S_Gulper.txt /Volumes/AUVCTD/surveys/2012/odv done.
INFO 2025-06-26 19:01:14,022 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.08/dorado_2012.143.08_processing.log /Volumes/AUVCTD/surveys/2012/netcdf