INFO 2025-06-26 15:27:20,894 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 15:27:20,895 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Kanna mission - Even though the thursdays runs (3 of them) are very short (~30mn each) the first one at leas had the gulper fired so it is of relevance for further science analysis. - ctdToUse = ctd1 INFO 2025-06-26 15:27:20,895 process.py process_mission():449 [1] Processing AUVCTD mission 2009.309.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:27:20,895 process.py download_process():165 [1] Download and processing steps for 2009.309.00 INFO 2025-06-26 15:27:20,895 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009309/2009.309.00 INFO 2025-06-26 15:27:20,895 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009309/2009.309.00 to /data/auv_data/dorado/missionlogs/2009.309.00 INFO 2025-06-26 15:27:22,270 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.309.00 INFO 2025-06-26 15:27:22,270 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/ctdDriver.log (966814 bytes) INFO 2025-06-26 15:27:22,346 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/ctdDriver2.log (972613 bytes) INFO 2025-06-26 15:27:22,421 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/gps.log (56588 bytes) INFO 2025-06-26 15:27:22,435 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/hydroscatlog.log (935698 bytes) INFO 2025-06-26 15:27:22,553 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/navigation.log (3257398 bytes) INFO 2025-06-26 15:27:22,802 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/isuslog.log (64021 bytes) INFO 2025-06-26 15:27:22,813 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/parosci.log (1143398 bytes) INFO 2025-06-26 15:27:22,912 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/tailCone.log (143611 bytes) INFO 2025-06-26 15:27:22,937 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/biolume.log (762284 bytes) INFO 2025-06-26 15:27:23,012 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 15:27:23,054 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.78 seconds INFO 2025-06-26 15:27:23,054 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.00/lopc.bin (1760276 bytes) INFO 2025-06-26 15:27:23,054 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:27:23 2025 INFO 2025-06-26 15:27:23,055 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.309.00/parosci.nc INFO 2025-06-26 15:27:23,055 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:27:23,055 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.309.00/parosci.nc INFO 2025-06-26 15:27:23,057 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1257437247.7, sensor_off_time = 1257440037.0 INFO 2025-06-26 15:27:23,057 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 2789 seconds. Expecting to read 5578 L frames from the lopc.bin file. INFO 2025-06-26 15:27:23,057 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 5578 records from the lopc.bin file. INFO 2025-06-26 15:27:23,090 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-11-05 16:07:27 Z and endTime = 2009-11-05 16:53:56 Z with 5578 records expected to be read from lopc.bin INFO 2025-06-26 15:27:23,090 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.309.00/lopc.bin INFO 2025-06-26 15:27:23,090 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.309.00/lopc.nc INFO 2025-06-26 15:27:23,091 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.309.00/lopc.nc INFO 2025-06-26 15:27:23,091 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.309.00 INFO 2025-06-26 15:27:23,092 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 15:27:23,135 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:27:23,135 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:27:23,135 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 15:27:24,634 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 15:27:24,634 process.py calibrate():227 [1] Calibration steps for 2009.309.00 INFO 2025-06-26 15:27:24,714 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 15:27:24,716 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:27:25,456 calibrate.py _nudge_pos():1806 [1] 106: 0.130 0.0032743 -0.0002529 10085 33.61 14.458 -1.394 2009-11-05T16:42:46.465604608 INFO 2025-06-26 15:27:25,549 calibrate.py _nudge_pos():1806 [1] 116: 0.120 -0.0000063 -0.0000046 20 0.06 -14.873 -13.316 2009-11-05T16:42:59.464713984 INFO 2025-06-26 15:27:31,700 calibrate.py _nudge_pos():1862 [1] 741: - - - 2 0.00 - - INFO 2025-06-26 15:27:31,700 calibrate.py _nudge_pos():1868 [1] Points in final series = 13794 WARNING 2025-06-26 15:27:31,722 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:27:31,840 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:27:32,033 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 44 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:27:32,124 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 44 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:27:32,126 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.309.00/ctd1.nc INFO 2025-06-26 15:27:32,127 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 15:27:32,127 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 15:27:32,128 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:27:32,238 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:27:32,322 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:27:32,324 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.309.00/ctd2.nc INFO 2025-06-26 15:27:32,325 calibrate.py _range_qc_combined_nc():898 [1] Setting 153 ctd2_salinity values to NaN INFO 2025-06-26 15:27:32,325 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 15:27:32,325 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 15:27:32,336 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 15:27:32,455 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 180 80700 122340 122341] INFO 2025-06-26 15:27:32,482 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 15:27:32,487 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 15:27:32,487 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2009.309.00 ERROR 2025-06-26 15:27:32,487 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.309.00 INFO 2025-06-26 15:27:32,493 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_cal.nc INFO 2025-06-26 15:27:32,540 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 15:27:32,546 process.py align():251 [1] Alignment steps for 2009.309.00 INFO 2025-06-26 15:27:32,570 align.py process_cal():139 [1] Processing dorado_2009.309.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.309.00 INFO 2025-06-26 15:27:32,578 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:32,580 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:32,598 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:32,600 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:32,617 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:32,619 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:32,629 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:27:32,629 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:27:32,636 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:27:32,638 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:27:32,655 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,657 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,673 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,675 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,690 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,693 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,709 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,711 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,727 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,730 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,745 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,748 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,763 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,765 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,780 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,782 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,798 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,800 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,815 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,818 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,834 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,836 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,852 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,855 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,872 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,874 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,891 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,893 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,909 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,911 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,927 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,929 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,945 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,947 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,964 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,966 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:32,982 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:32,984 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:33,001 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:27:33,003 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:27:33,025 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:27:33,044 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:27:33,061 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:27:33,079 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 15:27:33,097 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.07 INFO 2025-06-26 15:27:33,108 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_align.nc INFO 2025-06-26 15:27:33,153 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 15:27:33,155 process.py resample():273 [1] Resampling steps for 2009.309.00 INFO 2025-06-26 15:27:33,156 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:27:33,178 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_align.nc mission netCDF file INFO 2025-06-26 15:27:33,183 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_align.nc mission netCDF file INFO 2025-06-26 15:27:33,184 resample.py get_mission_start_end():1145 [1] navigation: 2009-11-05T16:07:58.308653056 to 2009-11-05T16:53:56.859679488 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 15:27:33,185 resample.py get_mission_start_end():1145 [1] hs2 : 2009-11-05T16:07:34.130309376 to 2009-11-05T16:53:56.919675392 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 15:27:33,187 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-11-05T16:08:12.387688704 to 2009-11-05T16:53:56.809682944 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 15:27:33,188 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-11-05T16:07:55.548842240 to 2009-11-05T16:53:56.979671296 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:27:33,190 resample.py get_mission_start_end():1145 [1] isus : 2009-11-05T16:08:44.955457792 to 2009-11-05T16:53:55.819750912 (0 days 00:00:01.159920384 before mission_end) INFO 2025-06-26 15:27:33,191 resample.py get_mission_start_end():1145 [1] biolume : 2009-11-05T16:07:25.380874752 to 2009-11-05T16:53:55.919709696 (0 days 00:00:01.059961600 before mission_end) INFO 2025-06-26 15:27:33,192 resample.py get_mission_start_end():1145 [1] tailcone : 2009-11-05T16:07:26.830809600 to 2009-11-05T16:53:56.539701504 (0 days 00:00:00.439969792 before mission_end) INFO 2025-06-26 15:27:33,193 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_align.nc mission netCDF file INFO 2025-06-26 15:27:33,193 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,247 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,258 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,270 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,281 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,293 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,304 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,315 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,326 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,336 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,346 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,355 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,365 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,375 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,384 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,394 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,403 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,415 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,426 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,437 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,448 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,460 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,471 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,481 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,490 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,498 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,508 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,518 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:27:33,626 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_1S.nc INFO 2025-06-26 15:27:34,911 create_products.py gulper_odv():401 [1] No gulper times found for 2009.309.00 INFO 2025-06-26 15:27:34,912 process.py archive():337 [1] Archiving steps for 2009.309.00 INFO 2025-06-26 15:27:34,912 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00, BASE_PATH = /data/auv_data INFO 2025-06-26 15:27:34,912 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:27:34,913 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.309.00_1S.nc INFO 2025-06-26 15:27:34,922 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:27:34,923 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.309.00_cal.nc INFO 2025-06-26 15:27:34,940 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:27:34,941 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.309.00_align.nc INFO 2025-06-26 15:27:34,957 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:27:34,966 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:34,974 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:34,978 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:34,985 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:34,998 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:35,003 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:35,010 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:35,015 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:35,027 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:35,038 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.00 done. INFO 2025-06-26 15:27:35,038 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:27:35,038 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.00/dorado_2009.309.00_processing.log /Volumes/AUVCTD/surveys/2009/netcdf