INFO 2025-06-26 21:44:41,768 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2015 --end_year 2025 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 21:44:41,768 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2015 - ctdToUse = ctd1 INFO 2025-06-26 21:44:41,768 process.py process_mission():449 [1] Processing CANON September 2015 mission 2015.287.00 by user docker_user on host 355841a7028c INFO 2025-06-26 21:44:41,768 process.py download_process():165 [1] Download and processing steps for 2015.287.00 INFO 2025-06-26 21:44:41,768 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2015/2015287/2015.287.00 INFO 2025-06-26 21:44:41,769 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2015/2015287/2015.287.00 to /data/auv_data/dorado/missionlogs/2015.287.00 INFO 2025-06-26 21:44:46,256 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2015.287.00 INFO 2025-06-26 21:44:46,256 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/ctdDriver.log (8980230 bytes) INFO 2025-06-26 21:44:46,913 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/ctdDriver2.log (8981663 bytes) INFO 2025-06-26 21:44:47,564 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/gps.log (86900 bytes) INFO 2025-06-26 21:44:47,582 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/hydroscatlog.log (7868638 bytes) INFO 2025-06-26 21:44:48,382 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2015.287.00/hydroscatlog.log: [ 1 2 4 5 6 8 10 11 13 14 15 16 17 19 21 22 23 25 26 27 30 33 34 35 37 39 41 42] INFO 2025-06-26 21:44:48,409 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/navigation.log (33669378 bytes) INFO 2025-06-26 21:44:50,872 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/isuslog.log (580309 bytes) INFO 2025-06-26 21:44:50,932 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/parosci.log (11028182 bytes) INFO 2025-06-26 21:44:51,886 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/tailCone.log (5621899 bytes) INFO 2025-06-26 21:44:52,578 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/biolume.log (6543782 bytes) INFO 2025-06-26 21:44:53,212 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 21:44:53,537 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.28 seconds INFO 2025-06-26 21:44:53,538 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2015.287.00/lopc.bin (34256122 bytes) INFO 2025-06-26 21:44:53,538 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 21:44:53 2025 INFO 2025-06-26 21:44:53,539 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2015.287.00/parosci.nc INFO 2025-06-26 21:44:53,539 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 21:44:53,539 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2015.287.00/parosci.nc INFO 2025-06-26 21:44:53,542 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1444836889.9, sensor_off_time = 1444860313.4 INFO 2025-06-26 21:44:53,542 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 23423 seconds. Expecting to read 46846 L frames from the lopc.bin file. INFO 2025-06-26 21:44:53,542 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 46846 records from the lopc.bin file. INFO 2025-06-26 21:44:53,868 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2015-10-14 15:34:49 Z and endTime = 2015-10-14 22:05:13 Z with 46846 records expected to be read from lopc.bin INFO 2025-06-26 21:44:53,868 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2015.287.00/lopc.bin INFO 2025-06-26 21:44:53,868 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2015.287.00/lopc.nc INFO 2025-06-26 21:44:53,868 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2015.287.00/lopc.nc INFO 2025-06-26 21:44:53,869 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2015.287.00 INFO 2025-06-26 21:44:53,869 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 21:44:53,902 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 21:44:53,902 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 21:44:53,902 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 21:44:58,016 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10000 8986 0 0 0 0 0 4.1 seconds, last L Frame: 46846 ERROR 2025-06-26 21:44:58,688 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 21:44:58,689 process.py calibrate():227 [1] Calibration steps for 2015.287.00 INFO 2025-06-26 21:44:58,890 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 21:44:58,892 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 21:45:00,053 calibrate.py _nudge_pos():1806 [1] 159: 0.060 -0.0002137 -0.0003795 1895 6.31 -5.024 -11.138 2015-10-14T15:43:44.679419648 INFO 2025-06-26 21:45:00,147 calibrate.py _nudge_pos():1806 [1] 169: 0.060 0.0000018 -0.0000079 245 0.81 0.332 -1.799 2015-10-14T15:44:42.675447040 INFO 2025-06-26 21:45:01,571 calibrate.py _nudge_pos():1806 [1] 321: 0.070 -0.0019666 -0.0017026 12755 42.51 -6.866 -7.421 2015-10-14T16:29:44.680346880 INFO 2025-06-26 21:45:01,639 calibrate.py _nudge_pos():1806 [1] 328: 0.060 -0.0000690 0.0000237 135 0.45 -22.921 9.842 2015-10-14T16:30:17.678086400 INFO 2025-06-26 21:45:02,902 calibrate.py _nudge_pos():1806 [1] 462: 0.070 -0.0044228 -0.0025742 6820 22.73 -28.880 -20.986 2015-10-14T16:55:14.675534848 INFO 2025-06-26 21:45:03,848 calibrate.py _nudge_pos():1806 [1] 561: 0.070 -0.0015357 -0.0025537 9530 31.76 -7.175 -14.898 2015-10-14T17:28:38.678251520 INFO 2025-06-26 21:45:04,433 calibrate.py _nudge_pos():1806 [1] 622: 0.070 -0.0065883 -0.0006110 13320 44.40 -22.013 -2.550 2015-10-14T18:14:02.681644544 INFO 2025-06-26 21:45:04,641 calibrate.py _nudge_pos():1806 [1] 644: 0.070 -0.0000111 -0.0000064 65 0.21 -7.693 -5.540 2015-10-14T18:14:37.679246848 INFO 2025-06-26 21:45:05,358 calibrate.py _nudge_pos():1806 [1] 720: 0.070 -0.0076653 -0.0041804 12685 42.28 -26.895 -18.321 2015-10-14T18:58:10.680243968 INFO 2025-06-26 21:45:06,129 calibrate.py _nudge_pos():1806 [1] 800: 0.070 -0.0060820 -0.0000060 11355 37.85 -23.845 -0.029 2015-10-14T19:37:20.679258112 INFO 2025-06-26 21:45:06,215 calibrate.py _nudge_pos():1806 [1] 809: 0.080 0.0001106 -0.0001074 290 0.96 17.033 -20.655 2015-10-14T19:38:26.674737152 INFO 2025-06-26 21:45:06,843 calibrate.py _nudge_pos():1806 [1] 875: 0.080 -0.0027192 0.0010054 12933 43.11 -9.362 4.321 2015-10-14T20:22:38.683062016 INFO 2025-06-26 21:45:07,584 calibrate.py _nudge_pos():1806 [1] 952: 0.080 -0.0018731 0.0007396 7210 24.03 -11.573 5.703 2015-10-14T20:47:56.679072256 INFO 2025-06-26 21:45:08,769 calibrate.py _nudge_pos():1806 [1] 1074: 0.090 -0.0018041 -0.0004376 12030 40.10 -6.678 -2.022 2015-10-14T21:30:03.675961088 INFO 2025-06-26 21:45:08,953 calibrate.py _nudge_pos():1806 [1] 1093: 0.090 -0.0000740 -0.0000043 115 0.38 -28.888 -2.095 2015-10-14T21:30:44.673152768 INFO 2025-06-26 21:45:09,297 calibrate.py _nudge_pos():1806 [1] 1128: 0.090 -0.0011365 -0.0002244 9820 32.73 -5.152 -1.270 2015-10-14T22:04:02.676280064 INFO 2025-06-26 21:45:09,308 calibrate.py _nudge_pos():1806 [1] 1129: 0.090 -0.0011661 -0.0001402 25 0.08 -2162.991 -324.791 2015-10-14T22:04:07.675937536 INFO 2025-06-26 21:45:09,943 calibrate.py _nudge_pos():1862 [1] 1150: - - - 4 0.01 - - INFO 2025-06-26 21:45:09,943 calibrate.py _nudge_pos():1868 [1] Points in final series = 116899 INFO 2025-06-26 21:45:21,897 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 93634 INFO 2025-06-26 21:45:22,613 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 2 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:45:23,490 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 39 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:45:24,181 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 39 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:45:24,183 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2015.287.00/ctd1.nc INFO 2025-06-26 21:45:24,184 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 21:45:24,185 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 21:45:24,185 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 21:45:25,001 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:45:25,684 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:45:25,687 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2015.287.00/ctd2.nc WARNING 2025-06-26 21:45:25,689 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (26323) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 21:45:25,689 calibrate.py _range_qc_combined_nc():898 [1] Setting 26323 ctd2_salinity values to NaN INFO 2025-06-26 21:45:25,689 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 21:45:25,689 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 21:45:25,727 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 21:45:26,777 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64] INFO 2025-06-26 21:45:26,978 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 21:45:48,258 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2015.287.00 ERROR 2025-06-26 21:45:48,258 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2015.287.00 INFO 2025-06-26 21:45:48,349 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_cal.nc INFO 2025-06-26 21:45:48,510 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 21:45:48,517 process.py align():251 [1] Alignment steps for 2015.287.00 INFO 2025-06-26 21:45:48,560 align.py process_cal():139 [1] Processing dorado_2015.287.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2015.287.00 INFO 2025-06-26 21:45:48,594 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:45:48,598 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:45:48,675 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:45:48,680 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:45:48,754 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:45:48,761 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:45:48,808 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 21:45:48,808 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 21:45:48,839 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:45:48,844 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:45:48,921 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:48,925 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:48,993 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:48,998 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,064 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,069 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,134 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,139 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,206 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,210 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,277 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,281 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,346 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,351 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,416 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,421 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,487 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,492 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,557 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,562 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,629 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,634 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,700 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,704 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,771 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,776 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,841 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,845 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,914 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,919 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:49,987 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:49,993 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:50,062 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:50,067 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:50,133 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:50,138 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:50,207 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:50,212 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:50,277 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:50,283 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:50,350 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:50,355 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:50,425 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:45:50,429 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:45:50,514 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:45:50,571 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:45:50,629 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:45:50,690 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:45:50,751 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:45:50,859 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 21:45:51,473 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:45:51,526 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_align.nc INFO 2025-06-26 21:45:51,689 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 21:45:51,692 process.py resample():273 [1] Resampling steps for 2015.287.00 INFO 2025-06-26 21:45:51,692 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 21:45:51,730 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_align.nc mission netCDF file INFO 2025-06-26 21:45:51,737 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_align.nc mission netCDF file INFO 2025-06-26 21:45:51,738 resample.py get_mission_start_end():1145 [1] navigation: 2015-10-14T15:35:33.493068544 to 2015-10-14T22:05:13.481429504 (0 days 00:00:00 before mission_end) INFO 2025-06-26 21:45:51,740 resample.py get_mission_start_end():1145 [1] hs2 : 2015-10-14T15:34:52.815855104 to 2015-10-14T22:05:13.461430784 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 21:45:51,742 resample.py get_mission_start_end():1145 [1] ctd1 : 2015-10-14T15:35:29.583336448 to 2015-10-14T22:05:13.301441792 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 21:45:51,744 resample.py get_mission_start_end():1145 [1] ctd2 : 2015-10-14T15:35:25.463618560 to 2015-10-14T22:05:13.421433600 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 21:45:51,745 resample.py get_mission_start_end():1145 [1] isus : 2015-10-14T15:36:07.170761472 to 2015-10-14T22:05:13.051459072 (0 days 00:00:00.429970432 before mission_end) INFO 2025-06-26 21:45:51,747 resample.py get_mission_start_end():1145 [1] biolume : 2015-10-14T15:34:47.766166784 to 2015-10-14T22:05:12.401469184 (0 days 00:00:01.079960320 before mission_end) INFO 2025-06-26 21:45:51,748 resample.py get_mission_start_end():1145 [1] tailcone : 2015-10-14T15:34:51.105971968 to 2015-10-14T22:05:13.411434496 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 21:45:51,749 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_align.nc mission netCDF file INFO 2025-06-26 21:45:51,750 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,002 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,049 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,094 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,137 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,176 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,213 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,250 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,286 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,319 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,353 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,386 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,421 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,456 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,489 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,524 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,558 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,593 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,630 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,667 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,755 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,791 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,828 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,866 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,902 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,920 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,935 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,950 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,964 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,978 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:52,983 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 21:45:52,983 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 21:45:53,797 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 21:45:53,968 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 21:45:54,065 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 21:45:54,103 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 21:45:54,133 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 21:45:54,133 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 21:45:54,181 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 21:45:54,425 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_1S.nc INFO 2025-06-26 21:45:56,336 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 21:45:57,489 create_products.py gulper_odv():522 [1] Wrote 1 Gulper data lines to /data/auv_data/dorado/missionodvs/2015.287.00/dorado_2015.287.00_1S_Gulper.txt INFO 2025-06-26 21:45:57,489 process.py archive():337 [1] Archiving steps for 2015.287.00 INFO 2025-06-26 21:45:57,489 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00, BASE_PATH = /data/auv_data INFO 2025-06-26 21:45:57,491 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00 files to /Volumes/AUVCTD/surveys/2015/netcdf INFO 2025-06-26 21:45:57,492 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.287.00_1S.nc INFO 2025-06-26 21:45:57,514 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_1S.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:45:57,515 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.287.00_cal.nc INFO 2025-06-26 21:45:57,671 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_cal.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:45:57,672 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.287.00_align.nc INFO 2025-06-26 21:45:57,902 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_align.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:45:57,941 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:57,971 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:57,977 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,006 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,105 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,112 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,147 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,172 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,243 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,267 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015287/2015.287.00 done. INFO 2025-06-26 21:45:58,267 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 21:45:58,268 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2015/odv/dorado_2015.287.00_1S_Gulper.txt INFO 2025-06-26 21:45:58,272 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2015.287.00/dorado_2015.287.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2015/odv done. INFO 2025-06-26 21:45:58,273 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.287.00/dorado_2015.287.00_processing.log /Volumes/AUVCTD/surveys/2015/netcdf