INFO 2025-06-26 20:13:58,098 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 20:13:58,098 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Spring 2014 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:13:58,098 process.py process_mission():449 [1] Processing SIMZ Spring 2014 mission 2014.071.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:13:58,098 process.py download_process():165 [1] Download and processing steps for 2014.071.01 INFO 2025-06-26 20:13:58,098 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014071/2014.071.01 INFO 2025-06-26 20:13:58,098 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014071/2014.071.01 to /data/auv_data/dorado/missionlogs/2014.071.01 INFO 2025-06-26 20:14:00,787 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.071.01 INFO 2025-06-26 20:14:00,788 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/ctdDriver.log (2555718 bytes) INFO 2025-06-26 20:14:00,967 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/ctdDriver2.log (2536127 bytes) INFO 2025-06-26 20:14:01,151 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/gps.log (32540 bytes) INFO 2025-06-26 20:14:01,162 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/hydroscatlog.log (2240470 bytes) INFO 2025-06-26 20:14:01,400 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/navigation.log (9539874 bytes) INFO 2025-06-26 20:14:02,097 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/parosci.log (3150806 bytes) INFO 2025-06-26 20:14:02,360 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/tailCone.log (1601659 bytes) INFO 2025-06-26 20:14:02,561 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/biolume.log (1866302 bytes) INFO 2025-06-26 20:14:02,743 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:14:02,840 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.05 seconds INFO 2025-06-26 20:14:02,841 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.01/lopc.bin (32795660 bytes) INFO 2025-06-26 20:14:02,841 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:14:02 2025 INFO 2025-06-26 20:14:02,841 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.071.01/parosci.nc INFO 2025-06-26 20:14:02,841 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:14:02,841 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.071.01/parosci.nc INFO 2025-06-26 20:14:02,844 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1394638405.4, sensor_off_time = 1394645076.5 INFO 2025-06-26 20:14:02,844 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 6671 seconds. Expecting to read 13342 L frames from the lopc.bin file. INFO 2025-06-26 20:14:02,844 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 13342 records from the lopc.bin file. INFO 2025-06-26 20:14:02,923 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-03-12 15:33:25 Z and endTime = 2014-03-12 17:24:36 Z with 13342 records expected to be read from lopc.bin INFO 2025-06-26 20:14:02,923 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.071.01/lopc.bin INFO 2025-06-26 20:14:02,923 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.071.01/lopc.nc INFO 2025-06-26 20:14:02,924 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.071.01/lopc.nc INFO 2025-06-26 20:14:02,924 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.071.01 INFO 2025-06-26 20:14:02,924 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:14:03,026 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:14:03,026 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:14:03,026 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:14:03,532 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:14:03,533 process.py calibrate():227 [1] Calibration steps for 2014.071.01 INFO 2025-06-26 20:14:03,637 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 20:14:03,639 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:14:04,257 calibrate.py _nudge_pos():1806 [1] 106: 0.100 0.0000308 0.0007088 1835 6.11 0.746 21.485 2014-03-12T15:41:15.938559744 INFO 2025-06-26 20:14:04,775 calibrate.py _nudge_pos():1806 [1] 162: 0.100 0.0007112 0.0006950 8875 29.58 3.561 4.354 2014-03-12T16:11:45.943195904 INFO 2025-06-26 20:14:05,108 calibrate.py _nudge_pos():1806 [1] 198: 0.100 0.0007172 0.0008417 9155 30.51 3.482 5.111 2014-03-12T16:42:51.945366016 INFO 2025-06-26 20:14:05,492 calibrate.py _nudge_pos():1806 [1] 239: 0.100 0.0005869 0.0005988 7420 24.73 3.516 4.487 2014-03-12T17:08:15.940965120 INFO 2025-06-26 20:14:05,882 calibrate.py _nudge_pos():1806 [1] 281: 0.100 0.0004481 0.0001662 3905 13.01 5.102 2.367 2014-03-12T17:21:57.944654080 INFO 2025-06-26 20:14:07,343 calibrate.py _nudge_pos():1862 [1] 391: - - - 2 0.00 - - INFO 2025-06-26 20:14:07,343 calibrate.py _nudge_pos():1868 [1] Points in final series = 33116 INFO 2025-06-26 20:14:07,451 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 26660 INFO 2025-06-26 20:14:07,655 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:14:07,918 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:14:08,118 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:14:08,120 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.071.01/ctd1.nc INFO 2025-06-26 20:14:08,121 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:14:08,121 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 20:14:08,122 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:14:08,372 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 68 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:14:08,570 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 68 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:14:08,572 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.071.01/ctd2.nc INFO 2025-06-26 20:14:08,573 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:14:08,573 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 20:14:08,573 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:14:08,574 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.071.01 INFO 2025-06-26 20:14:08,579 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:14:08,991 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:14:09,008 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.071.01 ERROR 2025-06-26 20:14:09,008 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.071.01 INFO 2025-06-26 20:14:09,036 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_cal.nc INFO 2025-06-26 20:14:09,107 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 20:14:09,112 process.py align():251 [1] Alignment steps for 2014.071.01 INFO 2025-06-26 20:14:09,139 align.py process_cal():139 [1] Processing dorado_2014.071.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.071.01 INFO 2025-06-26 20:14:09,152 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:09,154 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:09,183 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:09,185 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:09,212 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:09,215 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:09,231 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:14:09,231 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:14:09,242 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:09,244 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:09,271 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,273 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,298 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,300 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,325 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,327 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,352 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,354 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,379 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,382 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,406 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,408 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,433 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,436 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,460 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,463 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,488 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,490 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,515 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,518 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,547 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,550 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,576 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,578 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,604 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,606 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,631 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,634 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,660 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,662 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,688 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,691 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,716 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,719 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,744 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,747 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,772 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,775 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,800 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,803 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,828 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,831 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,856 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:09,858 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:09,891 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:14:09,919 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:14:09,955 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:14:10,133 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:10,155 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_align.nc INFO 2025-06-26 20:14:10,229 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 20:14:10,231 process.py resample():273 [1] Resampling steps for 2014.071.01 INFO 2025-06-26 20:14:10,232 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:14:10,256 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_align.nc mission netCDF file INFO 2025-06-26 20:14:10,260 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_align.nc mission netCDF file INFO 2025-06-26 20:14:10,261 resample.py get_mission_start_end():1145 [1] navigation: 2014-03-12T15:34:13.357508352 to 2014-03-12T17:24:36.343802880 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 20:14:10,263 resample.py get_mission_start_end():1145 [1] hs2 : 2014-03-12T15:33:29.330524672 to 2014-03-12T17:24:36.283806976 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 20:14:10,264 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-03-12T15:33:42.909594368 to 2014-03-12T17:24:36.253808896 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 20:14:10,265 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-03-12T15:34:33.766110464 to 2014-03-12T17:24:36.363801600 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:14:10,267 resample.py get_mission_start_end():1145 [1] biolume : 2014-03-12T15:33:23.100916992 to 2014-03-12T17:24:34.973862400 (0 days 00:00:01.389939200 before mission_end) INFO 2025-06-26 20:14:10,268 resample.py get_mission_start_end():1145 [1] tailcone : 2014-03-12T15:33:25.120812800 to 2014-03-12T17:24:36.303805696 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:14:10,269 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_align.nc mission netCDF file INFO 2025-06-26 20:14:10,269 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,359 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,377 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,394 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,411 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,427 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,443 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,458 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,473 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,487 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,501 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,514 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,529 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,543 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,557 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,571 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,584 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,598 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,614 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,630 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,646 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,661 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,677 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,692 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,707 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,717 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,725 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:10,729 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:14:10,729 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:14:10,971 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:14:11,013 resample.py add_biolume_proxies():633 [1] Zero flow values found: 6672 of 6672 - replaced with 350 ml/s INFO 2025-06-26 20:14:11,014 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:14:11,040 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:14:11,051 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:14:11,062 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:14:11,062 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:14:11,085 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:11,223 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_1S.nc INFO 2025-06-26 20:14:13,188 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:14:22,850 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.071.01/dorado_2014.071.01_1S_Gulper.txt INFO 2025-06-26 20:14:22,850 process.py archive():337 [1] Archiving steps for 2014.071.01 INFO 2025-06-26 20:14:22,850 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:14:22,852 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:14:22,852 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.071.01_1S.nc INFO 2025-06-26 20:14:22,865 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:14:22,866 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.071.01_cal.nc INFO 2025-06-26 20:14:22,915 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:14:22,916 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.071.01_align.nc INFO 2025-06-26 20:14:22,986 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:14:23,000 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,012 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,017 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,028 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,055 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,068 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,079 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,100 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,106 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.01 done. INFO 2025-06-26 20:14:23,106 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:14:23,107 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.071.01_1S_Gulper.txt INFO 2025-06-26 20:14:23,111 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.071.01/dorado_2014.071.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:14:23,111 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.01/dorado_2014.071.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf