INFO 2025-06-26 20:12:32,539 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 20:12:32,540 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Spring 2014 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:12:32,540 process.py process_mission():449 [1] Processing SIMZ Spring 2014 mission 2014.050.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:12:32,540 process.py download_process():165 [1] Download and processing steps for 2014.050.00 INFO 2025-06-26 20:12:32,540 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014050/2014.050.00 INFO 2025-06-26 20:12:32,540 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014050/2014.050.00 to /data/auv_data/dorado/missionlogs/2014.050.00 INFO 2025-06-26 20:12:35,232 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.050.00 INFO 2025-06-26 20:12:35,233 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/ctdDriver.log (2715558 bytes) INFO 2025-06-26 20:12:35,432 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/ctdDriver2.log (2715455 bytes) INFO 2025-06-26 20:12:35,639 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/gps.log (32540 bytes) INFO 2025-06-26 20:12:35,651 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/hydroscatlog.log (2381422 bytes) INFO 2025-06-26 20:12:35,896 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/navigation.log (10152738 bytes) INFO 2025-06-26 20:12:36,622 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/parosci.log (3350774 bytes) INFO 2025-06-26 20:12:36,899 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/tailCone.log (1703467 bytes) INFO 2025-06-26 20:12:37,109 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/biolume.log (1985014 bytes) INFO 2025-06-26 20:12:37,306 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:12:37,408 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.18 seconds INFO 2025-06-26 20:12:37,409 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.00/lopc.bin (29660186 bytes) INFO 2025-06-26 20:12:37,409 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:12:37 2025 INFO 2025-06-26 20:12:37,409 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.050.00/parosci.nc INFO 2025-06-26 20:12:37,409 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:12:37,409 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.050.00/parosci.nc INFO 2025-06-26 20:12:37,412 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1392823878.3, sensor_off_time = 1392830973.7 INFO 2025-06-26 20:12:37,412 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 7095 seconds. Expecting to read 14190 L frames from the lopc.bin file. INFO 2025-06-26 20:12:37,412 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 14190 records from the lopc.bin file. INFO 2025-06-26 20:12:37,498 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-02-19 15:31:18 Z and endTime = 2014-02-19 17:29:33 Z with 14190 records expected to be read from lopc.bin INFO 2025-06-26 20:12:37,498 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.050.00/lopc.bin INFO 2025-06-26 20:12:37,498 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.050.00/lopc.nc INFO 2025-06-26 20:12:37,498 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.050.00/lopc.nc INFO 2025-06-26 20:12:37,499 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.050.00 INFO 2025-06-26 20:12:37,499 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:12:37,637 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:12:37,637 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:12:37,637 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:12:37,727 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:12:37,728 process.py calibrate():227 [1] Calibration steps for 2014.050.00 INFO 2025-06-26 20:12:37,836 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 20:12:37,838 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:12:38,517 calibrate.py _nudge_pos():1806 [1] 111: 0.170 0.0001061 -0.0000884 1065 3.55 4.432 -4.617 2014-02-19T15:36:40.101297152 INFO 2025-06-26 20:12:39,111 calibrate.py _nudge_pos():1806 [1] 175: 0.170 0.0014114 0.0003389 9795 32.65 6.403 1.923 2014-02-19T16:10:22.102780672 INFO 2025-06-26 20:12:39,605 calibrate.py _nudge_pos():1806 [1] 228: 0.180 0.0014979 0.0006425 9640 32.13 6.906 3.706 2014-02-19T16:43:22.107141120 INFO 2025-06-26 20:12:40,234 calibrate.py _nudge_pos():1806 [1] 291: 0.180 0.0013769 0.0002510 7880 26.26 7.768 1.771 2014-02-19T17:10:40.104930304 INFO 2025-06-26 20:12:40,737 calibrate.py _nudge_pos():1806 [1] 344: 0.190 0.0009631 0.0002206 4930 16.43 8.686 2.488 2014-02-19T17:27:58.103822592 INFO 2025-06-26 20:12:41,630 calibrate.py _nudge_pos():1862 [1] 392: - - - 3 0.01 - - INFO 2025-06-26 20:12:41,630 calibrate.py _nudge_pos():1868 [1] Points in final series = 35243 INFO 2025-06-26 20:12:41,961 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:12:42,240 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:12:42,458 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:12:42,460 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.050.00/ctd1.nc INFO 2025-06-26 20:12:42,461 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:12:42,461 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 20:12:42,461 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:12:42,736 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:12:42,948 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:12:42,950 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.050.00/ctd2.nc INFO 2025-06-26 20:12:42,951 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:12:42,952 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 20:12:42,952 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:12:42,952 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.050.00 INFO 2025-06-26 20:12:42,958 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:12:43,385 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:12:43,402 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.050.00 ERROR 2025-06-26 20:12:43,402 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.050.00 INFO 2025-06-26 20:12:43,432 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_cal.nc INFO 2025-06-26 20:12:43,506 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, 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 20:12:43,511 process.py align():251 [1] Alignment steps for 2014.050.00 INFO 2025-06-26 20:12:43,539 align.py process_cal():139 [1] Processing dorado_2014.050.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.050.00 INFO 2025-06-26 20:12:43,554 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:12:43,556 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:12:43,587 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:12:43,590 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:12:43,619 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:12:43,622 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:12:43,639 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:12:43,639 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:12:43,651 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:12:43,654 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:12:43,682 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,685 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,712 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,714 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,741 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,744 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,771 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,774 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,800 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,803 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,829 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,831 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,858 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,861 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,887 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,890 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,917 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,920 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,947 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,949 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:43,976 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:43,979 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,005 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,008 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,035 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,038 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,066 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,069 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,096 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,098 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,125 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,128 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,155 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,158 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,185 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,187 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,214 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,217 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,243 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,247 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,273 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,276 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,303 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:12:44,305 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:12:44,340 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:12:44,368 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:12:44,406 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:12:44,594 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:12:44,617 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_align.nc INFO 2025-06-26 20:12:44,694 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, 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 20:12:44,696 process.py resample():273 [1] Resampling steps for 2014.050.00 INFO 2025-06-26 20:12:44,696 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:12:44,721 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_align.nc mission netCDF file INFO 2025-06-26 20:12:44,726 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_align.nc mission netCDF file INFO 2025-06-26 20:12:44,727 resample.py get_mission_start_end():1145 [1] navigation: 2014-02-19T15:32:05.120134656 to 2014-02-19T17:29:33.707273216 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:12:44,728 resample.py get_mission_start_end():1145 [1] hs2 : 2014-02-19T15:31:25.732833024 to 2014-02-19T17:29:33.697273856 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 20:12:44,730 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-02-19T15:31:44.011580672 to 2014-02-19T17:29:33.597281024 (0 days 00:00:00.109992192 before mission_end) INFO 2025-06-26 20:12:44,731 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-02-19T15:31:44.241564928 to 2014-02-19T17:29:33.587281408 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 20:12:44,732 resample.py get_mission_start_end():1145 [1] biolume : 2014-02-19T15:31:16.463433472 to 2014-02-19T17:29:32.677309696 (0 days 00:00:01.029963520 before mission_end) INFO 2025-06-26 20:12:44,734 resample.py get_mission_start_end():1145 [1] tailcone : 2014-02-19T15:31:18.153351936 to 2014-02-19T17:29:33.547284480 (0 days 00:00:00.159988736 before mission_end) INFO 2025-06-26 20:12:44,734 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_align.nc mission netCDF file INFO 2025-06-26 20:12:44,735 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,829 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,847 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,866 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,883 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,900 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,916 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,933 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,949 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,964 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,978 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:44,992 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,007 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,022 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,036 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,051 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,065 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,080 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,096 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,111 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,127 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,142 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,157 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,172 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,188 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,197 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,205 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,209 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:12:45,209 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:12:45,474 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:12:45,518 resample.py add_biolume_proxies():633 [1] Zero flow values found: 7097 of 7097 - replaced with 350 ml/s INFO 2025-06-26 20:12:45,518 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:12:45,544 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:12:45,555 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:12:45,566 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:12:45,566 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:12:45,588 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:12:45,731 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_1S.nc INFO 2025-06-26 20:12:48,231 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:13:00,788 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.050.00/dorado_2014.050.00_1S_Gulper.txt INFO 2025-06-26 20:13:00,788 process.py archive():337 [1] Archiving steps for 2014.050.00 INFO 2025-06-26 20:13:00,788 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:13:00,790 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:13:00,791 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.050.00_1S.nc INFO 2025-06-26 20:13:00,803 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:13:00,804 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.050.00_cal.nc INFO 2025-06-26 20:13:00,854 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:13:00,855 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.050.00_align.nc INFO 2025-06-26 20:13:00,928 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:13:00,943 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:00,956 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:00,960 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:00,971 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:01,001 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:01,015 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:01,026 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:01,047 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:01,053 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.00 done. INFO 2025-06-26 20:13:01,053 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:13:01,055 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.050.00_1S_Gulper.txt INFO 2025-06-26 20:13:01,060 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.050.00/dorado_2014.050.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:13:01,060 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.00/dorado_2014.050.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf