INFO 2025-06-26 17:21:30,177 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 17:21:30,177 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Kanna mission with automated forwarding of stella104 position to TREX via MBARITracking/scripts/drifter.py RabbitMQ and Tom O'Reilly's Tracking APp - ctdToUse = ctd1 INFO 2025-06-26 17:21:30,177 process.py process_mission():449 [1] Processing AUVCTD mission 2011.060.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 17:21:30,177 process.py download_process():165 [1] Download and processing steps for 2011.060.01 INFO 2025-06-26 17:21:30,177 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011060/2011.060.01 INFO 2025-06-26 17:21:30,177 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011060/2011.060.01 to /data/auv_data/dorado/missionlogs/2011.060.01 INFO 2025-06-26 17:21:32,396 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.060.01 INFO 2025-06-26 17:21:32,396 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/ctdDriver.log (3295019 bytes) INFO 2025-06-26 17:21:32,627 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/ctdDriver2.log (3295007 bytes) INFO 2025-06-26 17:21:32,865 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/gps.log (170132 bytes) INFO 2025-06-26 17:21:32,891 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/hydroscatlog.log (2889706 bytes) INFO 2025-06-26 17:21:33,199 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/navigation.log (10098566 bytes) INFO 2025-06-26 17:21:33,916 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/isuslog.log (212245 bytes) INFO 2025-06-26 17:21:33,941 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/parosci.log (3503078 bytes) INFO 2025-06-26 17:21:34,249 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/tailCone.log (2065915 bytes) INFO 2025-06-26 17:21:34,507 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/biolume.log (2406470 bytes) INFO 2025-06-26 17:21:34,801 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 17:21:34,929 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.53 seconds INFO 2025-06-26 17:21:34,929 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.060.01/lopc.bin (7437000 bytes) INFO 2025-06-26 17:21:34,929 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 17:21:34 2025 INFO 2025-06-26 17:21:34,929 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.060.01/parosci.nc INFO 2025-06-26 17:21:34,929 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 17:21:34,929 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.060.01/parosci.nc INFO 2025-06-26 17:21:34,933 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1299012523.2, sensor_off_time = 1299021130.1 INFO 2025-06-26 17:21:34,933 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 8606 seconds. Expecting to read 17212 L frames from the lopc.bin file. INFO 2025-06-26 17:21:34,933 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 17212 records from the lopc.bin file. INFO 2025-06-26 17:21:35,034 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-03-01 20:48:43 Z and endTime = 2011-03-01 23:12:10 Z with 17212 records expected to be read from lopc.bin INFO 2025-06-26 17:21:35,034 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.060.01/lopc.bin INFO 2025-06-26 17:21:35,034 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.060.01/lopc.nc INFO 2025-06-26 17:21:35,034 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.060.01/lopc.nc INFO 2025-06-26 17:21:35,035 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.060.01 INFO 2025-06-26 17:21:35,035 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 17:21:35,038 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A068177 WARNING 2025-06-26 17:21:35,038 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 17:21:35,080 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 17:21:35,080 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 17:21:35,080 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 17:21:40,010 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10344 11639 0 0 1 0 0 5.0 seconds, last L Frame: 17212 ERROR 2025-06-26 17:21:41,827 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 17:21:41,828 process.py calibrate():227 [1] Calibration steps for 2011.060.01 INFO 2025-06-26 17:21:41,949 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 17:21:41,950 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 17:21:46,021 calibrate.py _nudge_pos():1806 [1] 481: 0.140 0.0037140 -0.0041175 6710 22.36 24.638 -34.117 2011-03-01T21:19:04.968678912 INFO 2025-06-26 17:21:48,311 calibrate.py _nudge_pos():1806 [1] 730: 0.150 0.0005667 -0.0036439 8660 28.86 2.913 -23.394 2011-03-01T21:52:04.963040000 INFO 2025-06-26 17:21:49,491 calibrate.py _nudge_pos():1806 [1] 858: 0.150 -0.0002088 -0.0000953 1645 5.48 -5.651 -3.223 2011-03-01T21:59:40.961801984 INFO 2025-06-26 17:22:00,492 calibrate.py _nudge_pos():1806 [1] 2042: 0.150 -0.0017120 -0.0029058 6115 20.38 -12.461 -26.420 2011-03-01T22:39:46.966979328 INFO 2025-06-26 17:22:01,688 calibrate.py _nudge_pos():1806 [1] 2166: 0.150 0.0028279 -0.0028080 8175 27.25 15.398 -19.096 2011-03-01T23:09:04.966548224 INFO 2025-06-26 17:22:03,423 calibrate.py _nudge_pos():1862 [1] 2300: - - - 1 0.00 - - INFO 2025-06-26 17:22:03,423 calibrate.py _nudge_pos():1868 [1] Points in final series = 42781 WARNING 2025-06-26 17:22:03,566 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 17:22:03,888 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 17:22:04,221 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:22:04,479 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:22:04,480 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.060.01/ctd1.nc INFO 2025-06-26 17:22:04,481 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 17:22:04,482 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 17:22:04,482 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 17:22:04,796 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:22:05,056 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 17:22:05,058 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.060.01/ctd2.nc INFO 2025-06-26 17:22:05,060 calibrate.py _range_qc_combined_nc():898 [1] Setting 175 ctd2_salinity values to NaN INFO 2025-06-26 17:22:05,060 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 17:22:05,060 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 17:22:05,078 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 17:22:05,441 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 17:22:05,520 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 17:22:13,274 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.060.01 ERROR 2025-06-26 17:22:13,274 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.060.01 INFO 2025-06-26 17:22:13,310 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_cal.nc INFO 2025-06-26 17:22:13,399 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 17:22:13,406 process.py align():251 [1] Alignment steps for 2011.060.01 INFO 2025-06-26 17:22:13,438 align.py process_cal():139 [1] Processing dorado_2011.060.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.060.01 INFO 2025-06-26 17:22:13,454 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:22:13,457 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:22:13,493 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:22:13,496 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:22:13,531 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:22:13,535 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:22:13,555 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 17:22:13,556 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 17:22:13,570 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 17:22:13,573 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:22:13,608 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,611 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,643 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,646 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,677 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,680 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,712 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,715 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,746 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,749 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,781 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,785 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,817 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,820 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,852 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,855 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,889 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,892 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,924 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,927 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,960 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,963 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:13,994 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:13,997 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,030 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,033 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,064 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,067 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,099 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,102 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,134 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,137 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,170 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,174 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,206 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,209 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,242 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,245 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,277 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,280 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,312 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,316 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,348 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.060.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 17:22:14,351 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 17:22:14,390 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:22:14,420 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:22:14,450 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 17:22:14,482 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:22:14,514 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 17:22:14,553 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 17:22:14,784 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 17:22:14,812 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_align.nc INFO 2025-06-26 17:22:14,908 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 17:22:14,911 process.py resample():273 [1] Resampling steps for 2011.060.01 INFO 2025-06-26 17:22:14,912 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 17:22:14,941 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_align.nc mission netCDF file INFO 2025-06-26 17:22:14,947 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_align.nc mission netCDF file INFO 2025-06-26 17:22:14,949 resample.py get_mission_start_end():1145 [1] navigation: 2011-03-01T20:49:33.980000000 to 2011-03-01T23:12:10.163861248 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 17:22:14,950 resample.py get_mission_start_end():1145 [1] hs2 : 2011-03-01T20:48:49.113073664 to 2011-03-01T23:12:10.173860608 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 17:22:14,952 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-03-01T20:49:11.261556480 to 2011-03-01T23:12:10.063868160 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 17:22:14,954 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-03-01T20:49:11.521538560 to 2011-03-01T23:12:10.063868160 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 17:22:14,955 resample.py get_mission_start_end():1145 [1] isus : 2011-03-01T20:50:05.167863552 to 2011-03-01T23:12:09.093934592 (0 days 00:00:01.099924480 before mission_end) INFO 2025-06-26 17:22:14,957 resample.py get_mission_start_end():1145 [1] biolume : 2011-03-01T20:48:42.573487360 to 2011-03-01T23:12:08.813919488 (0 days 00:00:01.379939584 before mission_end) INFO 2025-06-26 17:22:14,958 resample.py get_mission_start_end():1145 [1] tailcone : 2011-03-01T20:48:44.383397632 to 2011-03-01T23:12:10.193859072 (0 days 00:00:00 before mission_end) INFO 2025-06-26 17:22:14,959 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_align.nc mission netCDF file INFO 2025-06-26 17:22:14,959 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,073 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,094 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,115 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,135 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,154 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,173 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,191 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,209 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,228 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,249 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,265 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,282 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,299 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,315 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,332 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,349 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,365 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,384 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,403 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,424 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,443 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,463 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,482 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,500 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,513 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,524 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,534 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,543 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,553 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:15,557 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 17:22:15,557 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 17:22:15,825 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 17:22:15,882 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 17:22:15,911 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 17:22:15,925 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 17:22:15,939 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 17:22:15,940 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 17:22:15,966 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 17:22:16,126 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_1S.nc INFO 2025-06-26 17:22:17,134 create_products.py gulper_odv():401 [1] No gulper times found for 2011.060.01 INFO 2025-06-26 17:22:17,134 process.py archive():337 [1] Archiving steps for 2011.060.01 INFO 2025-06-26 17:22:17,134 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01, BASE_PATH = /data/auv_data INFO 2025-06-26 17:22:17,134 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 17:22:17,139 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.060.01_1S.nc INFO 2025-06-26 17:22:17,154 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:22:17,156 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.060.01_cal.nc INFO 2025-06-26 17:22:17,214 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:22:17,215 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.060.01_align.nc INFO 2025-06-26 17:22:17,301 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 17:22:17,317 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,331 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,337 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,349 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,378 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,383 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,397 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,409 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,435 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,460 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011060/2011.060.01 done. INFO 2025-06-26 17:22:17,460 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 17:22:17,460 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.060.01/dorado_2011.060.01_processing.log /Volumes/AUVCTD/surveys/2011/netcdf