INFO 2025-06-26 19:51:02,030 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 19:51:02,030 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:51:02,030 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.274.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:51:02,031 process.py download_process():165 [1] Download and processing steps for 2013.274.01 INFO 2025-06-26 19:51:02,031 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013274/2013.274.01 INFO 2025-06-26 19:51:02,031 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013274/2013.274.01 to /data/auv_data/dorado/missionlogs/2013.274.01 INFO 2025-06-26 19:51:05,515 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.274.01 INFO 2025-06-26 19:51:05,515 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/ctdDriver.log (3078150 bytes) INFO 2025-06-26 19:51:05,735 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/ctdDriver2.log (3078335 bytes) INFO 2025-06-26 19:51:05,952 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/gps.log (118580 bytes) INFO 2025-06-26 19:51:05,972 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/hydroscatlog.log (2698606 bytes) INFO 2025-06-26 19:51:06,253 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/navigation.log (10892918 bytes) INFO 2025-06-26 19:51:07,015 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/isuslog.log (341 bytes) INFO 2025-06-26 19:51:07,019 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/parosci.log (3790982 bytes) INFO 2025-06-26 19:51:07,328 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.274.01/parosci.log: [9744] INFO 2025-06-26 19:51:07,337 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/tailCone.log (1930747 bytes) INFO 2025-06-26 19:51:07,574 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/biolume.log (2248850 bytes) INFO 2025-06-26 19:51:07,802 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:51:07,921 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.41 seconds INFO 2025-06-26 19:51:07,922 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.01/lopc.bin (13005825 bytes) INFO 2025-06-26 19:51:07,922 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:51:07 2025 INFO 2025-06-26 19:51:07,922 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.274.01/parosci.nc INFO 2025-06-26 19:51:07,922 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:51:07,922 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.274.01/parosci.nc INFO 2025-06-26 19:51:07,925 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1380651365.3, sensor_off_time = 1380659406.8 INFO 2025-06-26 19:51:07,926 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 8041 seconds. Expecting to read 16082 L frames from the lopc.bin file. INFO 2025-06-26 19:51:07,926 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 16082 records from the lopc.bin file. INFO 2025-06-26 19:51:08,019 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-01 18:16:05 Z and endTime = 2013-10-01 20:30:06 Z with 16082 records expected to be read from lopc.bin INFO 2025-06-26 19:51:08,020 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.274.01/lopc.bin INFO 2025-06-26 19:51:08,020 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.274.01/lopc.nc INFO 2025-06-26 19:51:08,020 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.274.01/lopc.nc INFO 2025-06-26 19:51:08,020 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.274.01 INFO 2025-06-26 19:51:08,021 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:51:08,023 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:51:08,123 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:51:08,123 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:51:08,123 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:51:10,037 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:51:10,037 process.py calibrate():227 [1] Calibration steps for 2013.274.01 INFO 2025-06-26 19:51:10,152 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 19:51:10,153 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:51:10,621 calibrate.py _nudge_pos():1806 [1] 79: 0.020 0.0001662 -0.0003498 1504 5.01 4.917 -12.927 2013-10-01T18:22:21.911348224 INFO 2025-06-26 19:51:11,529 calibrate.py _nudge_pos():1806 [1] 178: 0.030 -0.0010703 -0.0002943 9740 32.46 -4.889 -1.680 2013-10-01T18:56:27.911187968 INFO 2025-06-26 19:51:12,353 calibrate.py _nudge_pos():1806 [1] 267: 0.040 -0.0009396 -0.0002010 8050 26.83 -5.192 -1.388 2013-10-01T19:24:45.904867328 INFO 2025-06-26 19:51:12,382 calibrate.py _nudge_pos():1806 [1] 270: 0.030 0.0000091 -0.0000026 145 0.48 2.813 -1.011 2013-10-01T19:25:16.912743168 INFO 2025-06-26 19:51:13,143 calibrate.py _nudge_pos():1806 [1] 352: 0.040 -0.0011230 -0.0002613 9550 31.83 -5.230 -1.521 2013-10-01T19:58:27.906350592 INFO 2025-06-26 19:51:13,944 calibrate.py _nudge_pos():1806 [1] 438: 0.040 -0.0002356 -0.0001025 3085 10.28 -3.397 -1.848 2013-10-01T20:10:09.908260352 INFO 2025-06-26 19:51:25,144 calibrate.py _nudge_pos():1862 [1] 1599: - - - 4 0.01 - - INFO 2025-06-26 19:51:25,144 calibrate.py _nudge_pos():1868 [1] Points in final series = 40038 INFO 2025-06-26 19:51:26,726 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:51:27,106 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:51:27,350 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:51:27,352 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.274.01/ctd1.nc INFO 2025-06-26 19:51:27,353 calibrate.py _range_qc_combined_nc():898 [1] Setting 6 ctd1_salinity values to NaN INFO 2025-06-26 19:51:27,354 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 19:51:27,354 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:51:27,646 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:51:27,884 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:51:27,886 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.274.01/ctd2.nc INFO 2025-06-26 19:51:27,887 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:51:27,888 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 19:51:27,888 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:51:27,900 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:51:28,239 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71] INFO 2025-06-26 19:51:28,313 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:51:35,578 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.274.01 ERROR 2025-06-26 19:51:35,579 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.274.01 INFO 2025-06-26 19:51:35,613 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_cal.nc INFO 2025-06-26 19:51:35,696 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, 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 19:51:35,702 process.py align():251 [1] Alignment steps for 2013.274.01 INFO 2025-06-26 19:51:35,732 align.py process_cal():139 [1] Processing dorado_2013.274.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.274.01 INFO 2025-06-26 19:51:35,747 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:51:35,749 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:51:35,782 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:51:35,785 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:51:35,816 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:51:35,819 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:51:35,838 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:51:35,838 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:51:35,851 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:51:35,853 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:51:35,884 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:35,887 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:35,915 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:35,918 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:35,946 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:35,949 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:35,977 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:35,979 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,008 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,011 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,039 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,042 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,071 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,074 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,103 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,105 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,134 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,136 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,164 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,167 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,196 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,198 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,226 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,229 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,260 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,263 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,292 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,294 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,323 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,326 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,355 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,358 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,387 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,390 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,418 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,421 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,451 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,453 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,483 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,486 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,516 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,519 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,548 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:51:36,551 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:51:36,587 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.01 INFO 2025-06-26 19:51:36,612 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.01 INFO 2025-06-26 19:51:36,636 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.01 INFO 2025-06-26 19:51:36,662 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:51:36,700 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:51:36,742 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:51:36,959 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:51:36,985 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_align.nc INFO 2025-06-26 19:51:37,072 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, 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 19:51:37,075 process.py resample():273 [1] Resampling steps for 2013.274.01 INFO 2025-06-26 19:51:37,075 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:51:37,104 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_align.nc mission netCDF file INFO 2025-06-26 19:51:37,109 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_align.nc mission netCDF file INFO 2025-06-26 19:51:37,110 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-01T18:16:38.924844544 to 2013-10-01T20:30:06.706274048 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 19:51:37,111 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-01T18:16:14.126543616 to 2013-10-01T20:30:06.646278144 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 19:51:37,112 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-01T18:16:32.815262976 to 2013-10-01T20:30:06.686275584 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 19:51:37,114 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-01T18:16:32.335296000 to 2013-10-01T20:30:06.686275584 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 19:51:37,115 resample.py get_mission_start_end():1145 [1] isus : 2013-10-01T18:18:33.646985472 to 2013-10-01T18:21:11.876146176 (0 days 02:08:54.850126336 before mission_end) WARNING 2025-06-26 19:51:37,116 resample.py get_mission_start_end():1156 [1] Instrument isus has a gap > 5 minutes at the end of the mission: 0 days 02:08:54.850126336 INFO 2025-06-26 19:51:37,117 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-01T18:16:04.457171456 to 2013-10-01T20:30:06.146278144 (0 days 00:00:00.579994368 before mission_end) INFO 2025-06-26 19:51:37,118 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-01T18:16:03.937241344 to 2013-10-01T20:30:06.726272512 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:51:37,119 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_align.nc mission netCDF file INFO 2025-06-26 19:51:37,119 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,223 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,242 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,261 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,279 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,297 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,313 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,330 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,346 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,361 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,376 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,391 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,406 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,422 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,437 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,451 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,466 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,482 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,498 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,515 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,532 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,548 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,565 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,581 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,598 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,607 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,607 resample.py resample_variable():1038 [1] Padding isus_nitrate with 0 days 02:08:54.850126336 of NaNs to the end of mission INFO 2025-06-26 19:51:37,616 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,616 resample.py resample_variable():1038 [1] Padding isus_temp with 0 days 02:08:54.850126336 of NaNs to the end of mission INFO 2025-06-26 19:51:37,624 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,624 resample.py resample_variable():1038 [1] Padding isus_quality with 0 days 02:08:54.850126336 of NaNs to the end of mission INFO 2025-06-26 19:51:37,633 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,642 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:37,646 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:51:37,646 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:51:37,927 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:51:37,975 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:51:38,004 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:51:38,017 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:51:38,030 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:51:38,030 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:51:38,054 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:51:38,210 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_1S.nc INFO 2025-06-26 19:51:40,275 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:51:50,969 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.274.01/dorado_2013.274.01_1S_Gulper.txt INFO 2025-06-26 19:51:50,970 process.py archive():337 [1] Archiving steps for 2013.274.01 INFO 2025-06-26 19:51:50,970 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:51:50,971 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:51:50,972 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.274.01_1S.nc INFO 2025-06-26 19:51:50,986 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:51:50,987 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.274.01_cal.nc INFO 2025-06-26 19:51:51,048 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:51:51,049 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.274.01_align.nc INFO 2025-06-26 19:51:51,134 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:51:51,148 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,160 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,165 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,177 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,207 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,211 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,226 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,237 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,262 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,270 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.01 done. INFO 2025-06-26 19:51:51,271 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:51:51,272 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.274.01_1S_Gulper.txt INFO 2025-06-26 19:51:51,276 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.274.01/dorado_2013.274.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:51:51,277 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.01/dorado_2013.274.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf