INFO 2025-06-26 20:16:34,291 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:16:34,291 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:16:34,291 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.102.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:16:34,291 process.py download_process():165 [1] Download and processing steps for 2014.102.00 INFO 2025-06-26 20:16:34,291 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014102/2014.102.00 INFO 2025-06-26 20:16:34,291 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014102/2014.102.00 to /data/auv_data/dorado/missionlogs/2014.102.00 INFO 2025-06-26 20:16:37,396 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.102.00 INFO 2025-06-26 20:16:37,396 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/ctdDriver.log (4413030 bytes) INFO 2025-06-26 20:16:37,716 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/ctdDriver2.log (4419359 bytes) INFO 2025-06-26 20:16:38,024 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/gps.log (67964 bytes) INFO 2025-06-26 20:16:38,042 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/hydroscatlog.log (3872842 bytes) INFO 2025-06-26 20:16:38,436 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/navigation.log (16540866 bytes) INFO 2025-06-26 20:16:39,596 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/isuslog.log (286389 bytes) INFO 2025-06-26 20:16:39,628 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/parosci.log (5434502 bytes) INFO 2025-06-26 20:16:40,079 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/tailCone.log (2768251 bytes) INFO 2025-06-26 20:16:40,421 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/biolume.log (3224390 bytes) INFO 2025-06-26 20:16:40,737 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:16:40,905 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.51 seconds INFO 2025-06-26 20:16:40,905 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.102.00/lopc.bin (41672431 bytes) INFO 2025-06-26 20:16:40,905 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:16:40 2025 INFO 2025-06-26 20:16:40,905 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.102.00/parosci.nc INFO 2025-06-26 20:16:40,905 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:16:40,905 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.102.00/parosci.nc INFO 2025-06-26 20:16:40,909 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397314971.3, sensor_off_time = 1397326501.5 INFO 2025-06-26 20:16:40,909 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11530 seconds. Expecting to read 23060 L frames from the lopc.bin file. INFO 2025-06-26 20:16:40,909 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 23060 records from the lopc.bin file. INFO 2025-06-26 20:16:41,045 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-12 15:02:51 Z and endTime = 2014-04-12 18:15:01 Z with 23060 records expected to be read from lopc.bin INFO 2025-06-26 20:16:41,045 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.102.00/lopc.bin INFO 2025-06-26 20:16:41,045 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.102.00/lopc.nc INFO 2025-06-26 20:16:41,046 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.102.00/lopc.nc INFO 2025-06-26 20:16:41,046 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.102.00 INFO 2025-06-26 20:16:41,046 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:16:41,146 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:16:41,147 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:16:41,147 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:16:41,208 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:16:41,209 process.py calibrate():227 [1] Calibration steps for 2014.102.00 INFO 2025-06-26 20:16:41,354 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 20:16:41,355 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:16:41,951 calibrate.py _nudge_pos():1806 [1] 102: 0.010 0.0000427 0.0000901 925 3.08 2.141 5.422 2014-04-12T15:07:34.094265344 INFO 2025-06-26 20:16:41,961 calibrate.py _nudge_pos():1806 [1] 103: 0.200 0.0001267 0.0002642 44 0.14 136.389 341.605 2014-04-12T15:07:42.893662720 INFO 2025-06-26 20:16:42,239 calibrate.py _nudge_pos():1806 [1] 133: 0.010 0.0004291 -0.0000683 7340 24.46 2.707 -0.517 2014-04-12T15:32:40.091097856 INFO 2025-06-26 20:16:42,714 calibrate.py _nudge_pos():1806 [1] 184: 0.010 0.0004011 -0.0002200 10495 34.98 1.770 -1.165 2014-04-12T16:08:29.093880832 INFO 2025-06-26 20:16:43,250 calibrate.py _nudge_pos():1806 [1] 242: 0.020 -0.0002173 -0.0002394 7240 24.13 -1.390 -1.838 2014-04-12T16:33:34.090781696 INFO 2025-06-26 20:16:43,698 calibrate.py _nudge_pos():1806 [1] 290: 0.010 -0.0017860 -0.0005969 8705 29.01 -9.506 -3.812 2014-04-12T17:03:22.098294784 INFO 2025-06-26 20:16:43,941 calibrate.py _nudge_pos():1806 [1] 316: 0.020 -0.0010843 -0.0007855 7495 24.98 -6.704 -5.827 2014-04-12T17:28:46.093893888 INFO 2025-06-26 20:16:44,455 calibrate.py _nudge_pos():1806 [1] 371: 0.030 -0.0005890 -0.0015431 10740 35.80 -2.542 -7.988 2014-04-12T18:05:28.093046784 INFO 2025-06-26 20:16:44,494 calibrate.py _nudge_pos():1806 [1] 375: 0.030 0.0000248 -0.0000048 70 0.23 16.645 -3.897 2014-04-12T18:05:45.091881984 INFO 2025-06-26 20:16:49,750 calibrate.py _nudge_pos():1862 [1] 884: - - - 2 0.00 - - INFO 2025-06-26 20:16:49,751 calibrate.py _nudge_pos():1868 [1] Points in final series = 57326 INFO 2025-06-26 20:16:49,999 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 46093 INFO 2025-06-26 20:16:50,349 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:50,790 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 40 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:51,135 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 40 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:16:51,137 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.102.00/ctd1.nc INFO 2025-06-26 20:16:51,138 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:16:51,139 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 20:16:51,139 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:16:51,554 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:16:51,897 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:16:51,900 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.102.00/ctd2.nc INFO 2025-06-26 20:16:51,901 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:16:51,901 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 20:16:51,901 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:16:51,923 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:16:52,403 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62] INFO 2025-06-26 20:16:52,504 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 20:17:02,850 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.102.00 ERROR 2025-06-26 20:17:02,851 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.102.00 INFO 2025-06-26 20:17:02,897 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_cal.nc INFO 2025-06-26 20:17:02,997 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 20:17:03,002 process.py align():251 [1] Alignment steps for 2014.102.00 INFO 2025-06-26 20:17:03,036 align.py process_cal():139 [1] Processing dorado_2014.102.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.102.00 INFO 2025-06-26 20:17:03,055 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:03,058 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:03,103 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:03,106 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:03,151 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:03,155 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:03,180 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:17:03,180 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:17:03,197 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:03,201 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:03,245 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,248 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,288 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,292 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,330 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,333 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,370 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,373 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,412 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,415 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,453 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,456 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,495 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,498 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,537 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,541 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,579 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,583 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,620 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,624 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,662 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,665 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,702 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,706 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,744 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,748 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,785 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,788 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,827 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,831 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,869 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,873 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,912 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,916 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,953 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:03,957 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:03,996 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:04,000 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:04,039 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:04,043 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:04,082 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:04,086 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:04,124 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.102.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:04,127 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:04,175 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:17:04,211 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:17:04,247 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:17:04,284 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:17:04,323 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:17:04,385 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:17:04,682 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:04,714 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_align.nc INFO 2025-06-26 20:17:04,816 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 20:17:04,819 process.py resample():273 [1] Resampling steps for 2014.102.00 INFO 2025-06-26 20:17:04,819 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:17:04,850 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_align.nc mission netCDF file INFO 2025-06-26 20:17:04,857 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_align.nc mission netCDF file INFO 2025-06-26 20:17:04,858 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-12T15:03:36.860517376 to 2014-04-12T18:15:01.493765888 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 20:17:04,860 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-12T15:02:54.333430528 to 2014-04-12T18:15:01.433769984 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 20:17:04,861 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-12T15:03:31.480885760 to 2014-04-12T18:15:01.483766528 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:17:04,863 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-12T15:03:15.032012544 to 2014-04-12T18:15:01.513764608 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 20:17:04,864 resample.py get_mission_start_end():1145 [1] isus : 2014-04-12T15:04:03.598685440 to 2014-04-12T18:15:01.423770624 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 20:17:04,865 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-12T15:02:46.543929856 to 2014-04-12T18:15:01.013764608 (0 days 00:00:00.529997824 before mission_end) INFO 2025-06-26 20:17:04,867 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-12T15:02:49.533759232 to 2014-04-12T18:15:01.543762432 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:17:04,867 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_align.nc mission netCDF file INFO 2025-06-26 20:17:04,868 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,003 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,029 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,053 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,078 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,100 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,122 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,143 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,164 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,183 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,203 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,222 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,242 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,261 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,280 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,300 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,320 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,339 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,360 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,381 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,402 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,422 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,443 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,463 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,484 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,496 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,508 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,519 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,529 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,539 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:05,542 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:17:05,542 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:17:05,956 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:17:06,029 resample.py add_biolume_proxies():633 [1] Zero flow values found: 11536 of 11536 - replaced with 350 ml/s INFO 2025-06-26 20:17:06,029 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:17:06,069 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:17:06,088 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:17:06,104 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:17:06,105 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:17:06,133 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:06,308 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_1S.nc INFO 2025-06-26 20:17:07,931 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:17:17,593 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.102.00/dorado_2014.102.00_1S_Gulper.txt INFO 2025-06-26 20:17:17,593 process.py archive():337 [1] Archiving steps for 2014.102.00 INFO 2025-06-26 20:17:17,593 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:17:17,595 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:17:17,595 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.102.00_1S.nc INFO 2025-06-26 20:17:17,611 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:17:17,612 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.102.00_cal.nc INFO 2025-06-26 20:17:17,698 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:17:17,699 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.102.00_align.nc INFO 2025-06-26 20:17:17,815 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:17:17,833 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,849 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,853 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,867 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,910 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,916 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,934 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,948 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,983 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,988 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014102/2014.102.00 done. INFO 2025-06-26 20:17:17,988 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:17:17,989 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.102.00_1S_Gulper.txt INFO 2025-06-26 20:17:17,994 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.102.00/dorado_2014.102.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:17:17,994 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.102.00/dorado_2014.102.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf