INFO 2025-06-26 21:41:07,867 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 21:41:07,867 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2015 - ctdToUse = ctd1 INFO 2025-06-26 21:41:07,867 process.py process_mission():449 [1] Processing CANON September 2015 mission 2015.285.00 by user docker_user on host 355841a7028c INFO 2025-06-26 21:41:07,867 process.py download_process():165 [1] Download and processing steps for 2015.285.00 INFO 2025-06-26 21:41:07,867 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2015/2015285/2015.285.00 INFO 2025-06-26 21:41:07,867 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2015/2015285/2015.285.00 to /data/auv_data/dorado/missionlogs/2015.285.00 INFO 2025-06-26 21:41:12,297 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2015.285.00 INFO 2025-06-26 21:41:12,297 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/ctdDriver.log (9107238 bytes) INFO 2025-06-26 21:41:13,376 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/ctdDriver2.log (9118751 bytes) INFO 2025-06-26 21:41:14,169 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/gps.log (73796 bytes) INFO 2025-06-26 21:41:14,190 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/hydroscatlog.log (7983298 bytes) INFO 2025-06-26 21:41:15,087 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2015.285.00/hydroscatlog.log: [ 3 5 6 7 9 11 12 13 14 15 17] INFO 2025-06-26 21:41:15,126 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/navigation.log (34173666 bytes) INFO 2025-06-26 21:41:17,898 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/isuslog.log (588917 bytes) INFO 2025-06-26 21:41:17,963 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/parosci.log (11192438 bytes) INFO 2025-06-26 21:41:18,962 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2015.285.00/parosci.log: [191931] INFO 2025-06-26 21:41:19,009 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/tailCone.log (5706091 bytes) INFO 2025-06-26 21:41:19,764 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/biolume.log (6641194 bytes) INFO 2025-06-26 21:41:20,442 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 21:41:20,824 logs2netcdfs.py download_process_logs():807 [1] Time to process: 8.53 seconds INFO 2025-06-26 21:41:20,825 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2015.285.00/lopc.bin (24231767 bytes) INFO 2025-06-26 21:41:20,825 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 21:41:20 2025 INFO 2025-06-26 21:41:20,825 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2015.285.00/parosci.nc INFO 2025-06-26 21:41:20,825 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 21:41:20,825 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2015.285.00/parosci.nc INFO 2025-06-26 21:41:20,829 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1444665440.6, sensor_off_time = 1444689213.6 INFO 2025-06-26 21:41:20,830 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 23773 seconds. Expecting to read 47546 L frames from the lopc.bin file. INFO 2025-06-26 21:41:20,830 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 47546 records from the lopc.bin file. INFO 2025-06-26 21:41:21,114 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2015-10-12 15:57:20 Z and endTime = 2015-10-12 22:33:33 Z with 47546 records expected to be read from lopc.bin INFO 2025-06-26 21:41:21,115 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2015.285.00/lopc.bin INFO 2025-06-26 21:41:21,115 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2015.285.00/lopc.nc INFO 2025-06-26 21:41:21,115 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2015.285.00/lopc.nc INFO 2025-06-26 21:41:21,116 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2015.285.00 INFO 2025-06-26 21:41:21,116 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 21:41:21,191 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 21:41:21,192 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 21:41:21,192 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 21:41:21,620 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 21:41:21,621 process.py calibrate():227 [1] Calibration steps for 2015.285.00 INFO 2025-06-26 21:41:21,877 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 21:41:21,879 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 21:41:22,736 calibrate.py _nudge_pos():1806 [1] 122: 0.180 -0.0009926 -0.0000013 2085 6.95 -21.212 -0.034 2015-10-12T16:06:14.834948864 INFO 2025-06-26 21:41:23,446 calibrate.py _nudge_pos():1806 [1] 198: 0.180 -0.0060078 -0.0018762 13394 44.65 -19.971 -7.787 2015-10-12T16:52:08.836286720 INFO 2025-06-26 21:41:24,066 calibrate.py _nudge_pos():1806 [1] 263: 0.180 -0.0065678 -0.0035325 8555 28.51 -34.187 -22.957 2015-10-12T17:21:44.834622720 INFO 2025-06-26 21:41:24,114 calibrate.py _nudge_pos():1806 [1] 268: 0.180 -0.0000184 -0.0000049 335 1.11 -2.452 -0.811 2015-10-12T17:22:55.829759232 INFO 2025-06-26 21:41:24,854 calibrate.py _nudge_pos():1806 [1] 340: 0.180 -0.0025292 -0.0030660 10030 33.43 -11.227 -16.995 2015-10-12T17:57:32.837474304 INFO 2025-06-26 21:41:25,520 calibrate.py _nudge_pos():1806 [1] 409: 0.200 -0.0063906 -0.0005948 14690 48.96 -19.361 -2.251 2015-10-12T18:47:38.831549696 INFO 2025-06-26 21:41:26,050 calibrate.py _nudge_pos():1806 [1] 465: 0.200 -0.0072306 -0.0044081 11960 39.86 -26.908 -20.491 2015-10-12T19:28:25.833918464 INFO 2025-06-26 21:41:26,711 calibrate.py _nudge_pos():1806 [1] 532: 0.200 -0.0058718 -0.0007322 11224 37.41 -23.290 -3.627 2015-10-12T20:06:56.835603968 INFO 2025-06-26 21:41:27,831 calibrate.py _nudge_pos():1806 [1] 641: 0.200 -0.0018565 0.0007250 12510 41.70 -6.609 3.222 2015-10-12T20:50:26.836806656 INFO 2025-06-26 21:41:29,343 calibrate.py _nudge_pos():1806 [1] 787: 0.200 -0.0014998 0.0006564 6832 22.78 -9.776 5.340 2015-10-12T21:15:38.833227776 INFO 2025-06-26 21:41:29,507 calibrate.py _nudge_pos():1806 [1] 802: 0.010 0.0000321 -0.0000513 140 0.46 10.275 -20.532 2015-10-12T21:16:21.030337024 INFO 2025-06-26 21:41:29,924 calibrate.py _nudge_pos():1806 [1] 843: 0.200 -0.0015746 -0.0005898 12519 41.73 -5.601 -2.619 2015-10-12T21:58:44.836074496 INFO 2025-06-26 21:41:30,922 calibrate.py _nudge_pos():1806 [1] 938: 0.200 -0.0006552 0.0002933 9594 31.98 -3.040 1.699 2015-10-12T22:32:17.838174464 INFO 2025-06-26 21:41:31,709 calibrate.py _nudge_pos():1862 [1] 967: - - - 8 0.02 - - INFO 2025-06-26 21:41:31,709 calibrate.py _nudge_pos():1868 [1] Points in final series = 118354 INFO 2025-06-26 21:41:48,609 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:41:49,534 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 58 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:41:50,250 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 58 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 21:41:50,253 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2015.285.00/ctd1.nc INFO 2025-06-26 21:41:50,254 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 21:41:50,255 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 21:41:50,255 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 21:41:51,108 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:41:51,815 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 21:41:51,818 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2015.285.00/ctd2.nc WARNING 2025-06-26 21:41:51,820 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (22380) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 21:41:51,820 calibrate.py _range_qc_combined_nc():898 [1] Setting 22380 ctd2_salinity values to NaN INFO 2025-06-26 21:41:51,820 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 21:41:51,821 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 21:41:51,860 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 21:41:53,006 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66] INFO 2025-06-26 21:41:53,219 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 21:42:15,538 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2015.285.00 ERROR 2025-06-26 21:42:15,538 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2015.285.00 INFO 2025-06-26 21:42:15,645 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_cal.nc INFO 2025-06-26 21:42:15,838 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 21:42:15,847 process.py align():251 [1] Alignment steps for 2015.285.00 INFO 2025-06-26 21:42:15,908 align.py process_cal():139 [1] Processing dorado_2015.285.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2015.285.00 INFO 2025-06-26 21:42:15,950 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:42:15,955 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:42:16,037 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:42:16,043 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:42:16,124 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:42:16,131 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:42:16,180 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 21:42:16,180 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 21:42:16,213 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 21:42:16,219 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:42:16,301 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,306 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,380 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,386 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,456 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,462 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,535 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,540 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,612 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,617 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,694 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,700 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,770 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,775 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,848 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,854 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:16,926 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:16,932 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,003 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,009 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,080 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,086 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,156 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,162 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,231 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,236 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,308 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,312 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,386 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,391 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,466 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,472 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,548 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,554 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,626 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,632 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,705 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,710 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,782 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,788 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,861 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,867 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:17,938 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2015.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 21:42:17,943 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 21:42:18,032 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:42:18,093 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:42:18,155 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 21:42:18,218 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:42:18,286 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 21:42:18,406 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.98 INFO 2025-06-26 21:42:19,062 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 21:42:19,121 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_align.nc INFO 2025-06-26 21:42:19,313 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 21:42:19,316 process.py resample():273 [1] Resampling steps for 2015.285.00 INFO 2025-06-26 21:42:19,317 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 21:42:19,363 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_align.nc mission netCDF file INFO 2025-06-26 21:42:19,372 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_align.nc mission netCDF file INFO 2025-06-26 21:42:19,374 resample.py get_mission_start_end():1145 [1] navigation: 2015-10-12T15:58:03.238625536 to 2015-10-12T22:33:33.632982272 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 21:42:19,376 resample.py get_mission_start_end():1145 [1] hs2 : 2015-10-12T15:57:30.310881024 to 2015-10-12T22:33:33.712976640 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 21:42:19,378 resample.py get_mission_start_end():1145 [1] ctd1 : 2015-10-12T15:58:19.497511680 to 2015-10-12T22:33:33.722976000 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 21:42:19,380 resample.py get_mission_start_end():1145 [1] ctd2 : 2015-10-12T15:57:48.659624448 to 2015-10-12T22:33:33.612983552 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 21:42:19,382 resample.py get_mission_start_end():1145 [1] isus : 2015-10-12T15:58:36.576341504 to 2015-10-12T22:33:33.732975360 (0 days 00:00:00 before mission_end) INFO 2025-06-26 21:42:19,383 resample.py get_mission_start_end():1145 [1] biolume : 2015-10-12T15:57:17.061754624 to 2015-10-12T22:33:32.443029504 (0 days 00:00:01.289945856 before mission_end) INFO 2025-06-26 21:42:19,385 resample.py get_mission_start_end():1145 [1] tailcone : 2015-10-12T15:57:20.601546240 to 2015-10-12T22:33:33.622982656 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 21:42:19,386 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_align.nc mission netCDF file INFO 2025-06-26 21:42:19,386 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,655 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,703 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,750 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,797 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,839 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,880 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,921 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,961 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:19,999 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,037 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,074 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,111 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,149 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,186 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,225 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,263 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,302 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,342 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,386 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,475 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,516 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,557 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,715 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,756 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,778 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,797 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,814 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,832 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,849 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:20,855 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 21:42:20,855 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 21:42:21,650 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 21:42:21,873 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 21:42:21,994 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 21:42:22,047 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 21:42:22,082 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 21:42:22,083 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 21:42:22,139 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 21:42:22,407 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_1S.nc INFO 2025-06-26 21:42:24,300 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 21:42:47,418 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2015.285.00/dorado_2015.285.00_1S_Gulper.txt INFO 2025-06-26 21:42:47,419 process.py archive():337 [1] Archiving steps for 2015.285.00 INFO 2025-06-26 21:42:47,419 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00, BASE_PATH = /data/auv_data INFO 2025-06-26 21:42:47,420 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00 files to /Volumes/AUVCTD/surveys/2015/netcdf INFO 2025-06-26 21:42:47,421 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.285.00_1S.nc INFO 2025-06-26 21:42:47,449 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_1S.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:42:47,450 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.285.00_cal.nc INFO 2025-06-26 21:42:47,635 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_cal.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:42:47,636 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2015/netcdf/dorado_2015.285.00_align.nc INFO 2025-06-26 21:42:47,906 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_align.nc /Volumes/AUVCTD/surveys/2015/netcdf done. INFO 2025-06-26 21:42:47,939 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:47,970 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:47,975 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,001 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,105 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,113 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,149 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,174 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,243 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,256 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2015/2015285/2015.285.00 done. INFO 2025-06-26 21:42:48,256 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 21:42:48,258 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2015/odv/dorado_2015.285.00_1S_Gulper.txt INFO 2025-06-26 21:42:48,268 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2015.285.00/dorado_2015.285.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2015/odv done. INFO 2025-06-26 21:42:48,269 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2015.285.00/dorado_2015.285.00_processing.log /Volumes/AUVCTD/surveys/2015/netcdf