INFO 2025-06-26 20:05:32,516 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 20:05:32,517 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:05:32,517 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.296.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:05:32,517 process.py download_process():165 [1] Download and processing steps for 2013.296.00 INFO 2025-06-26 20:05:32,517 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013296/2013.296.00 INFO 2025-06-26 20:05:32,517 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013296/2013.296.00 to /data/auv_data/dorado/missionlogs/2013.296.00 INFO 2025-06-26 20:05:35,581 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.296.00 INFO 2025-06-26 20:05:35,581 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/ctdDriver.log (3028038 bytes) INFO 2025-06-26 20:05:35,791 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/ctdDriver2.log (3027839 bytes) INFO 2025-06-26 20:05:36,016 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/gps.log (124772 bytes) INFO 2025-06-26 20:05:36,037 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/hydroscatlog.log (2654590 bytes) INFO 2025-06-26 20:05:36,311 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/navigation.log (10710950 bytes) INFO 2025-06-26 20:05:37,060 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/parosci.log (3735062 bytes) INFO 2025-06-26 20:05:37,383 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/tailCone.log (1898827 bytes) INFO 2025-06-26 20:05:37,615 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/biolume.log (2212214 bytes) INFO 2025-06-26 20:05:37,833 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:05:37,945 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.36 seconds INFO 2025-06-26 20:05:37,945 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.00/lopc.bin (16515597 bytes) INFO 2025-06-26 20:05:37,945 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:05:37 2025 INFO 2025-06-26 20:05:37,945 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.296.00/parosci.nc INFO 2025-06-26 20:05:37,945 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:05:37,945 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.296.00/parosci.nc INFO 2025-06-26 20:05:37,948 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382538762.3, sensor_off_time = 1382546671.6 INFO 2025-06-26 20:05:37,948 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 7909 seconds. Expecting to read 15818 L frames from the lopc.bin file. INFO 2025-06-26 20:05:37,948 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 15818 records from the lopc.bin file. INFO 2025-06-26 20:05:38,041 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-23 14:32:42 Z and endTime = 2013-10-23 16:44:31 Z with 15818 records expected to be read from lopc.bin INFO 2025-06-26 20:05:38,042 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.296.00/lopc.bin INFO 2025-06-26 20:05:38,042 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.296.00/lopc.nc INFO 2025-06-26 20:05:38,042 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.296.00/lopc.nc INFO 2025-06-26 20:05:38,043 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.296.00 INFO 2025-06-26 20:05:38,043 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:05:38,046 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:05:38,077 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:05:38,077 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:05:38,077 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:05:39,388 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:05:39,389 process.py calibrate():227 [1] Calibration steps for 2013.296.00 INFO 2025-06-26 20:05:39,500 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 20:05:39,502 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:05:39,988 calibrate.py _nudge_pos():1806 [1] 82: 0.120 0.0000288 -0.0000323 465 1.55 2.756 -3.875 2013-10-23T14:35:34.334980352 INFO 2025-06-26 20:05:39,999 calibrate.py _nudge_pos():1806 [1] 83: 0.110 0.0000344 0.0001642 50 0.16 31.147 186.089 2013-10-23T14:35:44.344294656 INFO 2025-06-26 20:05:40,388 calibrate.py _nudge_pos():1806 [1] 124: 0.120 0.0002339 0.0010541 9200 30.66 1.130 6.370 2013-10-23T15:07:04.335506432 INFO 2025-06-26 20:05:40,945 calibrate.py _nudge_pos():1806 [1] 184: 0.120 0.0000972 0.0010978 9065 30.21 0.476 6.733 2013-10-23T15:38:16.337265408 INFO 2025-06-26 20:05:41,373 calibrate.py _nudge_pos():1806 [1] 230: 0.120 0.0002879 0.0008357 7515 25.05 1.703 6.183 2013-10-23T16:04:04.341219840 INFO 2025-06-26 20:05:41,874 calibrate.py _nudge_pos():1806 [1] 283: 0.130 0.0002100 0.0002893 4690 15.63 1.991 3.429 2013-10-23T16:20:34.343400192 INFO 2025-06-26 20:05:55,212 calibrate.py _nudge_pos():1862 [1] 1684: - - - 1 0.00 - - INFO 2025-06-26 20:05:55,212 calibrate.py _nudge_pos():1868 [1] Points in final series = 39370 INFO 2025-06-26 20:05:55,641 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:55,951 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:05:56,189 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:05:56,190 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.296.00/ctd1.nc INFO 2025-06-26 20:05:56,192 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:05:56,192 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 20:05:56,192 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:05:56,480 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:56,716 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:56,718 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.296.00/ctd2.nc INFO 2025-06-26 20:05:56,719 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:05:56,719 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 20:05:56,719 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:05:56,720 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.296.00 INFO 2025-06-26 20:05:56,726 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:05:57,055 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75] INFO 2025-06-26 20:05:57,126 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:06:04,227 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.296.00 ERROR 2025-06-26 20:06:04,227 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.296.00 INFO 2025-06-26 20:06:04,260 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_cal.nc INFO 2025-06-26 20:06:04,339 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 20:06:04,344 process.py align():251 [1] Alignment steps for 2013.296.00 INFO 2025-06-26 20:06:04,374 align.py process_cal():139 [1] Processing dorado_2013.296.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.296.00 INFO 2025-06-26 20:06:04,389 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:04,391 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:04,424 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:04,427 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:04,459 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:04,461 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:04,481 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:06:04,481 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:06:04,493 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:04,496 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:04,527 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,530 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,559 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,562 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,591 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,594 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,623 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,626 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,656 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,659 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,688 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,690 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,720 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,723 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,752 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,755 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,783 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,786 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,815 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,819 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,848 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,851 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,880 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,883 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,911 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,914 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,943 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,946 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:04,976 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:04,979 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,008 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:05,012 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,042 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:05,045 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,075 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:05,078 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,108 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:05,111 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,139 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:05,142 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,172 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:05,175 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,204 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:05,206 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:05,243 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:06:05,272 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:06:05,314 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:06:05,527 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:05,552 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_align.nc INFO 2025-06-26 20:06:05,633 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 20:06:05,635 process.py resample():273 [1] Resampling steps for 2013.296.00 INFO 2025-06-26 20:06:05,636 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:06:05,663 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_align.nc mission netCDF file INFO 2025-06-26 20:06:05,667 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_align.nc mission netCDF file INFO 2025-06-26 20:06:05,668 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-23T14:33:17.754336768 to 2013-10-23T16:44:31.534945792 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 20:06:05,670 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-23T14:32:49.926243072 to 2013-10-23T16:44:31.414953984 (0 days 00:00:00.199986432 before mission_end) INFO 2025-06-26 20:06:05,671 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-23T14:33:08.284985600 to 2013-10-23T16:44:31.614940416 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:06:05,672 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-23T14:33:08.094998272 to 2013-10-23T16:44:31.414953984 (0 days 00:00:00.199986432 before mission_end) INFO 2025-06-26 20:06:05,674 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-23T14:32:39.836900096 to 2013-10-23T16:44:30.274998016 (0 days 00:00:01.339942400 before mission_end) INFO 2025-06-26 20:06:05,675 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-23T14:32:42.026784256 to 2013-10-23T16:44:31.544945152 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 20:06:05,676 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_align.nc mission netCDF file INFO 2025-06-26 20:06:05,676 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,778 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,798 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,816 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,836 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,854 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,871 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,887 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,903 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,918 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,933 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,948 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,963 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,978 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:05,993 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,008 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,023 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,038 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,055 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,072 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,088 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,105 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,121 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,138 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,154 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,164 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,173 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,177 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:06:06,177 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:06:06,471 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:06:06,519 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:06:06,549 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:06:06,562 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:06:06,574 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:06:06,575 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:06:06,598 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:06,744 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_1S.nc INFO 2025-06-26 20:06:08,666 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:06:18,543 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.296.00/dorado_2013.296.00_1S_Gulper.txt INFO 2025-06-26 20:06:18,544 process.py archive():337 [1] Archiving steps for 2013.296.00 INFO 2025-06-26 20:06:18,544 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:06:18,544 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:06:18,545 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.296.00_1S.nc INFO 2025-06-26 20:06:18,558 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:06:18,559 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.296.00_cal.nc INFO 2025-06-26 20:06:18,616 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:06:18,617 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.296.00_align.nc INFO 2025-06-26 20:06:18,698 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:06:18,712 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,725 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,729 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,741 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,769 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,783 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,794 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,818 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,825 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.00 done. INFO 2025-06-26 20:06:18,825 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:06:18,827 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.296.00_1S_Gulper.txt INFO 2025-06-26 20:06:18,831 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.296.00/dorado_2013.296.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:06:18,831 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.00/dorado_2013.296.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf