INFO 2025-06-26 20:15:12,926 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 20:15:12,926 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Spring 2014 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:15:12,927 process.py process_mission():449 [1] Processing SIMZ Spring 2014 mission 2014.072.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:15:12,927 process.py download_process():165 [1] Download and processing steps for 2014.072.00 INFO 2025-06-26 20:15:12,927 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014072/2014.072.00 INFO 2025-06-26 20:15:12,927 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014072/2014.072.00 to /data/auv_data/dorado/missionlogs/2014.072.00 INFO 2025-06-26 20:15:15,543 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.072.00 INFO 2025-06-26 20:15:15,543 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/ctdDriver.log (2637318 bytes) INFO 2025-06-26 20:15:15,725 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.072.00/ctdDriver.log: [1] INFO 2025-06-26 20:15:15,731 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/ctdDriver2.log (2643551 bytes) INFO 2025-06-26 20:15:15,918 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/gps.log (65012 bytes) INFO 2025-06-26 20:15:15,932 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/hydroscatlog.log (2319346 bytes) INFO 2025-06-26 20:15:16,171 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/navigation.log (9883746 bytes) INFO 2025-06-26 20:15:16,879 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/parosci.log (3262790 bytes) INFO 2025-06-26 20:15:17,146 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.072.00/parosci.log: [1360 1361] INFO 2025-06-26 20:15:17,153 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/tailCone.log (1658587 bytes) INFO 2025-06-26 20:15:17,356 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/biolume.log (1933042 bytes) INFO 2025-06-26 20:15:17,547 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:15:17,646 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.10 seconds INFO 2025-06-26 20:15:17,646 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.072.00/lopc.bin (31789912 bytes) INFO 2025-06-26 20:15:17,646 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:15:17 2025 INFO 2025-06-26 20:15:17,646 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.072.00/parosci.nc INFO 2025-06-26 20:15:17,646 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:15:17,646 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.072.00/parosci.nc INFO 2025-06-26 20:15:17,649 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1394725159.2, sensor_off_time = 1394732067.5 INFO 2025-06-26 20:15:17,649 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 6908 seconds. Expecting to read 13816 L frames from the lopc.bin file. INFO 2025-06-26 20:15:17,649 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 13816 records from the lopc.bin file. INFO 2025-06-26 20:15:17,731 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-03-13 15:39:19 Z and endTime = 2014-03-13 17:34:27 Z with 13816 records expected to be read from lopc.bin INFO 2025-06-26 20:15:17,731 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.072.00/lopc.bin INFO 2025-06-26 20:15:17,732 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.072.00/lopc.nc INFO 2025-06-26 20:15:17,732 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.072.00/lopc.nc INFO 2025-06-26 20:15:17,732 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.072.00 INFO 2025-06-26 20:15:17,732 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:15:17,768 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:15:17,768 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:15:17,768 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:15:18,786 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:15:18,787 process.py calibrate():227 [1] Calibration steps for 2014.072.00 INFO 2025-06-26 20:15:18,894 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 20:15:18,895 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:15:19,531 calibrate.py _nudge_pos():1806 [1] 107: 0.140 0.0000684 0.0001128 565 1.88 5.388 11.121 2014-03-13T15:42:56.977624064 INFO 2025-06-26 20:15:19,959 calibrate.py _nudge_pos():1806 [1] 154: 0.150 0.0007029 0.0009120 8860 29.53 3.525 5.723 2014-03-13T16:13:14.973082624 INFO 2025-06-26 20:15:20,500 calibrate.py _nudge_pos():1806 [1] 213: 0.150 0.0007769 0.0008811 9070 30.23 3.807 5.401 2014-03-13T16:44:26.974841856 INFO 2025-06-26 20:15:20,968 calibrate.py _nudge_pos():1806 [1] 264: 0.160 0.0006606 0.0007388 7430 24.76 3.953 5.529 2014-03-13T17:10:02.969618688 INFO 2025-06-26 20:15:21,520 calibrate.py _nudge_pos():1806 [1] 324: 0.150 0.0006544 0.0002484 4115 13.71 7.071 3.356 2014-03-13T17:24:44.979196928 INFO 2025-06-26 20:15:21,530 calibrate.py _nudge_pos():1806 [1] 325: 0.150 -0.0000413 -0.0000117 85 0.28 -21.883 -7.764 2014-03-13T17:25:01.978032640 INFO 2025-06-26 20:15:26,775 calibrate.py _nudge_pos():1862 [1] 844: - - - 2 0.00 - - INFO 2025-06-26 20:15:26,775 calibrate.py _nudge_pos():1868 [1] Points in final series = 34310 INFO 2025-06-26 20:15:28,134 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:15:30,081 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:15:30,287 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:15:30,289 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.072.00/ctd1.nc INFO 2025-06-26 20:15:30,290 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:15:30,290 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 20:15:30,290 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:15:30,554 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:15:30,760 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:15:30,762 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.072.00/ctd2.nc INFO 2025-06-26 20:15:30,763 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:15:30,763 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 20:15:30,763 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:15:30,763 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.072.00 INFO 2025-06-26 20:15:30,769 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:15:31,190 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:15:31,207 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.072.00 ERROR 2025-06-26 20:15:31,207 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.072.00 INFO 2025-06-26 20:15:31,237 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_cal.nc INFO 2025-06-26 20:15:32,979 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 20:15:32,984 process.py align():251 [1] Alignment steps for 2014.072.00 INFO 2025-06-26 20:15:33,013 align.py process_cal():139 [1] Processing dorado_2014.072.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.072.00 INFO 2025-06-26 20:15:33,027 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:15:33,029 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:15:33,060 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:15:33,063 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:15:33,092 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:15:33,095 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:15:33,112 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:15:33,112 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:15:33,124 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:15:33,126 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:15:33,155 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,157 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,184 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,186 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,213 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,215 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,241 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,244 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,271 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,273 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,300 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,302 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,329 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,332 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,358 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,361 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,387 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,390 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,416 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,419 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,445 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,447 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,473 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,476 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,503 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,505 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,535 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,539 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,570 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,572 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,599 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,602 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,628 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,631 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,657 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,660 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,687 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,690 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,717 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,720 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,747 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,750 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,777 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.072.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:15:33,780 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:15:33,814 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:15:33,842 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:15:33,880 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:15:34,066 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:15:34,090 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_align.nc INFO 2025-06-26 20:15:34,166 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 20:15:34,168 process.py resample():273 [1] Resampling steps for 2014.072.00 INFO 2025-06-26 20:15:34,169 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:15:34,194 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_align.nc mission netCDF file INFO 2025-06-26 20:15:34,199 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_align.nc mission netCDF file INFO 2025-06-26 20:15:34,200 resample.py get_mission_start_end():1145 [1] navigation: 2014-03-13T15:40:05.579365376 to 2014-03-13T17:34:27.379299840 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 20:15:34,201 resample.py get_mission_start_end():1145 [1] hs2 : 2014-03-13T15:39:24.992145664 to 2014-03-13T17:34:27.449295104 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 20:15:34,202 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-03-13T15:40:01.969612544 to 2014-03-13T17:34:27.529289728 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:15:34,204 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-03-13T15:39:45.390748416 to 2014-03-13T17:34:27.469293824 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:15:34,205 resample.py get_mission_start_end():1145 [1] biolume : 2014-03-13T15:39:16.272708864 to 2014-03-13T17:34:26.899298560 (0 days 00:00:00.629991168 before mission_end) INFO 2025-06-26 20:15:34,206 resample.py get_mission_start_end():1145 [1] tailcone : 2014-03-13T15:39:19.122547968 to 2014-03-13T17:34:27.519290368 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 20:15:34,207 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_align.nc mission netCDF file INFO 2025-06-26 20:15:34,207 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,300 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,318 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,335 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,352 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,369 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,386 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,402 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,418 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,432 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,446 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,461 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,475 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,489 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,503 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,517 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,531 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,545 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,561 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,577 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,593 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,609 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,625 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,640 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,656 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,665 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,674 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:34,677 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:15:34,677 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:15:34,938 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:15:34,983 resample.py add_biolume_proxies():633 [1] Zero flow values found: 6911 of 6911 - replaced with 350 ml/s INFO 2025-06-26 20:15:34,983 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:15:35,010 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:15:35,022 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:15:35,033 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:15:35,033 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:15:35,056 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:35,199 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_1S.nc INFO 2025-06-26 20:15:37,103 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:15:46,737 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.072.00/dorado_2014.072.00_1S_Gulper.txt INFO 2025-06-26 20:15:46,738 process.py archive():337 [1] Archiving steps for 2014.072.00 INFO 2025-06-26 20:15:46,738 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:15:46,739 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:15:46,740 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.072.00_1S.nc INFO 2025-06-26 20:15:46,750 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:15:46,751 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.072.00_cal.nc INFO 2025-06-26 20:15:46,801 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:15:46,801 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.072.00_align.nc INFO 2025-06-26 20:15:46,870 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:15:46,884 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,896 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,900 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,910 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,936 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,949 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,960 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,985 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,992 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014072/2014.072.00 done. INFO 2025-06-26 20:15:46,992 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:15:46,994 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.072.00_1S_Gulper.txt INFO 2025-06-26 20:15:46,998 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.072.00/dorado_2014.072.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:15:46,998 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.072.00/dorado_2014.072.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf