INFO 2025-06-27 02:29:37,495 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 2025-06-27 02:29:37,495 process.py process_mission():434 [1] dorado_info[mission]["comment"] = MBTS mission - Overnight diamond in Monterey Bay - 24520G - first one with ecopuck instrument: FLBBCD2K - had to restart mission, 2 missions (245.00 and 246.01) required to complete the diamond QC note: Best CTD is ctd1 - ctdToUse = ctd1 INFO 2025-06-27 02:29:37,495 process.py process_mission():449 [1] Processing Monterey Bay Diamond mission 2020.245.00 by user docker_user on host 355841a7028c INFO 2025-06-27 02:29:37,495 process.py download_process():165 [1] Download and processing steps for 2020.245.00 INFO 2025-06-27 02:29:37,495 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2020/2020245/2020.245.00 INFO 2025-06-27 02:29:37,496 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2020/2020245/2020.245.00 to /data/auv_data/dorado/missionlogs/2020.245.00 INFO 2025-06-27 02:29:45,804 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2020.245.00 INFO 2025-06-27 02:29:45,804 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/ctdDriver.log (8846598 bytes) INFO 2025-06-27 02:29:46,482 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/ctdDriver2.log (8852925 bytes) INFO 2025-06-27 02:29:47,171 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/gps.log (609692 bytes) INFO 2025-06-27 02:29:47,242 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/hydroscatlog.log (7750282 bytes) INFO 2025-06-27 02:29:48,126 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/navigation.log (34102966 bytes) INFO 2025-06-27 02:29:50,717 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/isuslog.log (575381 bytes) INFO 2025-06-27 02:29:50,777 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/parosci.log (11023814 bytes) INFO 2025-06-27 02:29:51,716 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2020.245.00/parosci.log: [94210] INFO 2025-06-27 02:29:51,757 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/FLBBCD2K.log (739575 bytes) INFO 2025-06-27 02:29:51,858 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2020.245.00/FLBBCD2K.log: [ 1 2 3 5 6 7 8 9 10 11 12 13 14 15 16 20 28 37] INFO 2025-06-27 02:29:51,862 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/tailCone.log (5538811 bytes) INFO 2025-06-27 02:29:52,556 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/biolume.log (6446938 bytes) INFO 2025-06-27 02:29:53,184 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-27 02:29:53,514 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.71 seconds INFO 2025-06-27 02:29:53,515 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2020.245.00/lopc.bin (54778820 bytes) INFO 2025-06-27 02:29:53,515 lopcToNetCDF.py main():2297 [1] Processing begun: Fri Jun 27 02:29:53 2025 INFO 2025-06-27 02:29:53,515 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2020.245.00/parosci.nc INFO 2025-06-27 02:29:53,515 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-27 02:29:53,515 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2020.245.00/parosci.nc INFO 2025-06-27 02:29:53,518 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1598988566.1, sensor_off_time = 1599011642.5 INFO 2025-06-27 02:29:53,518 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 23076 seconds. Expecting to read 46152 L frames from the lopc.bin file. INFO 2025-06-27 02:29:53,518 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 46152 records from the lopc.bin file. INFO 2025-06-27 02:29:53,788 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2020-09-01 19:29:26 Z and endTime = 2020-09-02 01:54:02 Z with 46152 records expected to be read from lopc.bin INFO 2025-06-27 02:29:53,788 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2020.245.00/lopc.bin INFO 2025-06-27 02:29:53,788 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2020.245.00/lopc.nc INFO 2025-06-27 02:29:53,788 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2020.245.00/lopc.nc INFO 2025-06-27 02:29:53,789 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2020.245.00 INFO 2025-06-27 02:29:53,789 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-27 02:29:53,847 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-27 02:29:53,847 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-27 02:29:53,847 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-27 02:29:53,990 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-27 02:29:53,991 process.py calibrate():227 [1] Calibration steps for 2020.245.00 INFO 2025-06-27 02:29:54,197 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 2025-06-27 02:29:54,199 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-27 02:29:54,849 calibrate.py _nudge_pos():1806 [1] 100: 0.010 -0.0004978 0.0005813 6216 20.72 -3.565 5.200 2020-09-01T19:51:44.008826112 INFO 2025-06-27 02:29:54,994 calibrate.py _nudge_pos():1806 [1] 115: 0.060 -0.0001421 0.0000141 140 0.46 -45.523 5.636 2020-09-01T19:52:26.005948928 INFO 2025-06-27 02:29:56,874 calibrate.py _nudge_pos():1806 [1] 313: 0.130 -0.0003445 0.0000754 2605 8.68 -5.889 1.609 2020-09-01T20:04:24.006762752 INFO 2025-06-27 02:29:57,067 calibrate.py _nudge_pos():1806 [1] 333: 0.130 0.0000879 0.0000541 130 0.43 30.342 23.306 2020-09-01T20:05:09.003680256 INFO 2025-06-27 02:29:58,999 calibrate.py _nudge_pos():1806 [1] 536: 0.170 -0.0002257 0.0000855 2715 9.05 -3.702 1.750 2020-09-01T20:17:34.002644224 INFO 2025-06-27 02:30:01,315 calibrate.py _nudge_pos():1806 [1] 776: 0.080 -0.0000422 0.0003125 7271 24.23 -0.259 2.389 2020-09-01T20:45:47.206651904 INFO 2025-06-27 02:30:04,510 calibrate.py _nudge_pos():1806 [1] 1099: 0.050 -0.0030937 0.0015490 8826 29.42 -15.608 9.757 2020-09-01T21:20:34.403668992 INFO 2025-06-27 02:30:05,175 calibrate.py _nudge_pos():1806 [1] 1166: 0.180 -0.0021808 0.0002514 9160 30.53 -10.604 1.526 2020-09-01T21:52:12.403647232 INFO 2025-06-27 02:30:07,540 calibrate.py _nudge_pos():1806 [1] 1408: 0.140 -0.0020992 0.0008606 9390 31.30 -9.959 5.095 2020-09-01T22:27:31.608471552 INFO 2025-06-27 02:30:11,300 calibrate.py _nudge_pos():1806 [1] 1792: 0.090 -0.0016708 0.0005528 8126 27.08 -9.162 3.782 2020-09-01T23:00:59.800900864 INFO 2025-06-27 02:30:14,123 calibrate.py _nudge_pos():1806 [1] 2083: 0.040 -0.0019784 0.0007174 9186 30.62 -9.599 4.342 2020-09-01T23:36:27.005177600 INFO 2025-06-27 02:30:15,099 calibrate.py _nudge_pos():1806 [1] 2184: 0.200 -0.0021015 0.0009166 9415 31.38 -9.951 5.413 2020-09-02T00:09:30.009332480 INFO 2025-06-27 02:31:18,843 calibrate.py _nudge_pos():1862 [1] 8416: - - - 5 0.01 - - INFO 2025-06-27 02:31:18,843 calibrate.py _nudge_pos():1868 [1] Points in final series = 114796 INFO 2025-06-27 02:31:22,788 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 5 of 92253 INFO 2025-06-27 02:31:23,491 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 1 seconds, d_end_time_diff: -1 seconds INFO 2025-06-27 02:31:24,363 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 39 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 02:31:25,049 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 39 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 02:31:25,052 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2020.245.00/ctd1.nc INFO 2025-06-27 02:31:25,053 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-27 02:31:25,053 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 2025-06-27 02:31:25,053 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-27 02:31:25,886 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 02:31:26,574 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 02:31:26,576 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2020.245.00/ctd2.nc INFO 2025-06-27 02:31:26,578 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-27 02:31:26,578 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 2025-06-27 02:31:26,578 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-27 02:31:26,617 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-27 02:31:27,880 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-27 02:31:27,918 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2020.245.00 INFO 2025-06-27 02:31:28,994 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_cal.nc INFO 2025-06-27 02:31:29,164 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_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_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 2025-06-27 02:31:29,170 process.py align():251 [1] Alignment steps for 2020.245.00 INFO 2025-06-27 02:31:29,217 align.py process_cal():139 [1] Processing dorado_2020.245.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2020.245.00 INFO 2025-06-27 02:31:29,252 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 02:31:29,256 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 02:31:29,340 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 02:31:29,346 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 02:31:29,427 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 02:31:29,434 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 02:31:29,482 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-27 02:31:29,482 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-27 02:31:29,513 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 02:31:29,519 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 02:31:29,598 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:29,603 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:29,672 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:29,677 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:29,745 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:29,750 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:29,818 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:29,823 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:29,892 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:29,896 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:29,964 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:29,969 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,040 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,045 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,113 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,118 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,187 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,192 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,260 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,266 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,336 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,341 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,409 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,414 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,484 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,489 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,556 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,560 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,629 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,634 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,702 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,707 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,778 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,783 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,852 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,858 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:30,930 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:30,936 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:31,005 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:31,011 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:31,084 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:31,090 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:31,160 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:31,165 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:31,236 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.245.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 02:31:31,241 align.py process_cal():249 [1] ctd2_par: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 02:31:31,327 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 02:31:31,388 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 02:31:31,447 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 02:31:31,510 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-27 02:31:31,575 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-27 02:31:31,675 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.98 INFO 2025-06-27 02:31:32,250 align.py process_cal():249 [1] ecopuck_bbp700: instrument_sample_rate_hz = 0.89 INFO 2025-06-27 02:31:32,314 align.py process_cal():249 [1] ecopuck_cdom: instrument_sample_rate_hz = 0.89 INFO 2025-06-27 02:31:32,376 align.py process_cal():249 [1] ecopuck_chl: instrument_sample_rate_hz = 0.89 INFO 2025-06-27 02:31:32,439 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 02:31:32,494 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_align.nc INFO 2025-06-27 02:31:32,669 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_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_depth, ecopuck_latitude, ecopuck_longitude, ecopuck_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 2025-06-27 02:31:32,673 process.py resample():273 [1] Resampling steps for 2020.245.00 INFO 2025-06-27 02:31:32,674 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-27 02:31:32,716 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_align.nc mission netCDF file INFO 2025-06-27 02:31:32,723 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_align.nc mission netCDF file INFO 2025-06-27 02:31:32,725 resample.py get_mission_start_end():1145 [1] navigation: 2020-09-01T19:30:02.008019200 to 2020-09-02T01:54:02.609629952 (0 days 00:00:00 before mission_end) INFO 2025-06-27 02:31:32,727 resample.py get_mission_start_end():1145 [1] hs2 : 2020-09-01T19:29:27.350393600 to 2020-09-02T01:54:02.509636864 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-27 02:31:32,728 resample.py get_mission_start_end():1145 [1] ctd1 : 2020-09-01T19:30:05.447783680 to 2020-09-02T01:54:02.579632128 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-27 02:31:32,730 resample.py get_mission_start_end():1145 [1] ctd2 : 2020-09-01T19:29:48.648934400 to 2020-09-02T01:54:02.549634048 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-27 02:31:32,732 resample.py get_mission_start_end():1145 [1] isus : 2020-09-01T19:30:41.375322368 to 2020-09-02T01:54:01.769687296 (0 days 00:00:00.839942656 before mission_end) INFO 2025-06-27 02:31:32,733 resample.py get_mission_start_end():1145 [1] biolume : 2020-09-01T19:29:21.390767616 to 2020-09-02T01:54:02.029635328 (0 days 00:00:00.579994624 before mission_end) INFO 2025-06-27 02:31:32,735 resample.py get_mission_start_end():1145 [1] ecopuck : 2020-09-01T19:29:21.170817024 to 2020-09-02T01:54:02.149661440 (0 days 00:00:00.459968512 before mission_end) INFO 2025-06-27 02:31:32,737 resample.py get_mission_start_end():1145 [1] tailcone : 2020-09-01T19:29:26.550448128 to 2020-09-02T01:54:02.539634688 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-27 02:31:32,737 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_align.nc mission netCDF file INFO 2025-06-27 02:31:32,738 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:32,991 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,035 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,077 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,119 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,158 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,198 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,235 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,272 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,307 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,341 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,375 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,409 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,443 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,477 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,511 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,545 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,579 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,615 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,653 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,690 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,725 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,761 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,796 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,832 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,868 resample.py resample_variable():1031 [1] Resampling ctd2_par with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,887 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,902 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,917 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,931 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,945 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:33,951 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-27 02:31:33,951 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-27 02:31:34,736 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-27 02:31:34,891 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-27 02:31:34,974 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-27 02:31:35,012 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-27 02:31:35,043 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-27 02:31:35,043 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-27 02:31:35,066 resample.py resample_variable():1031 [1] Resampling ecopuck_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:35,082 resample.py resample_variable():1031 [1] Resampling ecopuck_cdom with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:35,098 resample.py resample_variable():1031 [1] Resampling ecopuck_chl with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:35,140 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-27 02:31:35,396 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_1S.nc INFO 2025-06-27 02:31:39,902 create_products.py _get_best_ctd():375 [1] Best CTD is ctd1 INFO 2025-06-27 02:31:52,669 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2020.245.00/dorado_2020.245.00_1S_Gulper.txt INFO 2025-06-27 02:31:52,669 process.py archive():337 [1] Archiving steps for 2020.245.00 INFO 2025-06-27 02:31:52,669 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00, BASE_PATH = /data/auv_data INFO 2025-06-27 02:31:52,675 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00 files to /Volumes/AUVCTD/surveys/2020/netcdf INFO 2025-06-27 02:31:52,678 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.245.00_1S.nc INFO 2025-06-27 02:31:52,782 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_1S.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 02:31:52,784 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.245.00_cal.nc INFO 2025-06-27 02:31:53,276 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_cal.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 02:31:53,280 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.245.00_align.nc INFO 2025-06-27 02:31:54,048 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_align.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 02:31:54,418 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:54,467 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:54,486 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:54,553 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:54,724 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:54,750 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:54,822 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:54,843 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/FLBBCD2K.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:55,013 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:55,132 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:55,165 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020245/2020.245.00 done. INFO 2025-06-27 02:31:55,165 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-27 02:31:55,170 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2020/odv/dorado_2020.245.00_1S_Gulper.txt INFO 2025-06-27 02:31:55,192 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2020.245.00/dorado_2020.245.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2020/odv done. INFO 2025-06-27 02:31:55,192 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.245.00/dorado_2020.245.00_processing.log /Volumes/AUVCTD/surveys/2020/netcdf