INFO 2025-06-26 20:20:53,632 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 20:20:53,632 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:20:53,633 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.108.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:20:53,633 process.py download_process():165 [1] Download and processing steps for 2014.108.01 INFO 2025-06-26 20:20:53,633 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014108/2014.108.01 INFO 2025-06-26 20:20:53,633 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014108/2014.108.01 to /data/auv_data/dorado/missionlogs/2014.108.01 INFO 2025-06-26 20:20:57,143 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.108.01 INFO 2025-06-26 20:20:57,143 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/ctdDriver.log (4157766 bytes) INFO 2025-06-26 20:20:57,436 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/ctdDriver2.log (4154975 bytes) INFO 2025-06-26 20:20:57,728 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/gps.log (37580 bytes) INFO 2025-06-26 20:20:57,740 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/hydroscatlog.log (3642598 bytes) INFO 2025-06-26 20:20:58,109 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/navigation.log (15551010 bytes) INFO 2025-06-26 20:20:59,212 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/isuslog.log (268629 bytes) INFO 2025-06-26 20:20:59,244 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/parosci.log (5111606 bytes) INFO 2025-06-26 20:20:59,678 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/tailCone.log (2603131 bytes) INFO 2025-06-26 20:20:59,991 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/biolume.log (3031838 bytes) INFO 2025-06-26 20:21:00,285 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:21:00,436 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.29 seconds INFO 2025-06-26 20:21:00,437 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.01/lopc.bin (33318124 bytes) INFO 2025-06-26 20:21:00,437 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:21:00 2025 INFO 2025-06-26 20:21:00,437 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.108.01/parosci.nc INFO 2025-06-26 20:21:00,437 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:21:00,437 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.108.01/parosci.nc INFO 2025-06-26 20:21:00,440 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397833532.0, sensor_off_time = 1397844375.9 INFO 2025-06-26 20:21:00,440 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10843 seconds. Expecting to read 21686 L frames from the lopc.bin file. INFO 2025-06-26 20:21:00,440 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21686 records from the lopc.bin file. INFO 2025-06-26 20:21:00,568 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-18 15:05:31 Z and endTime = 2014-04-18 18:06:15 Z with 21686 records expected to be read from lopc.bin INFO 2025-06-26 20:21:00,568 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.108.01/lopc.bin INFO 2025-06-26 20:21:00,568 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.108.01/lopc.nc INFO 2025-06-26 20:21:00,568 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.108.01/lopc.nc INFO 2025-06-26 20:21:00,569 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.108.01 INFO 2025-06-26 20:21:00,569 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:21:00,620 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:21:00,620 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:21:00,620 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:21:06,632 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:21:06,633 process.py calibrate():227 [1] Calibration steps for 2014.108.01 INFO 2025-06-26 20:21:06,763 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 20:21:06,765 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:21:07,459 calibrate.py _nudge_pos():1806 [1] 106: 0.140 -0.0006142 0.0003054 1955 6.51 -14.568 8.689 2014-04-18T15:13:45.972537856 INFO 2025-06-26 20:21:08,003 calibrate.py _nudge_pos():1806 [1] 164: 0.140 -0.0055682 0.0021894 10005 33.35 -25.788 12.166 2014-04-18T15:48:03.971555328 INFO 2025-06-26 20:21:08,525 calibrate.py _nudge_pos():1806 [1] 220: 0.150 -0.0058797 0.0028231 10075 33.58 -27.034 15.578 2014-04-18T16:22:33.969750528 INFO 2025-06-26 20:21:09,007 calibrate.py _nudge_pos():1806 [1] 272: 0.150 -0.0048050 0.0023597 10095 33.65 -22.043 12.996 2014-04-18T16:57:03.967945984 INFO 2025-06-26 20:21:09,552 calibrate.py _nudge_pos():1806 [1] 330: 0.160 -0.0037278 0.0015013 9435 31.45 -18.294 8.846 2014-04-18T17:29:27.964773120 INFO 2025-06-26 20:21:10,068 calibrate.py _nudge_pos():1806 [1] 385: 0.160 -0.0030523 0.0015405 8370 27.90 -16.883 10.232 2014-04-18T17:58:15.966396928 INFO 2025-06-26 20:21:10,087 calibrate.py _nudge_pos():1806 [1] 387: 0.170 -0.0000227 0.0000035 115 0.38 -9.211 1.703 2014-04-18T17:58:39.964752896 INFO 2025-06-26 20:21:10,567 calibrate.py _nudge_pos():1806 [1] 438: 0.160 -0.0002225 0.0008547 1670 5.56 -6.172 28.468 2014-04-18T18:05:03.968446976 INFO 2025-06-26 20:21:11,240 calibrate.py _nudge_pos():1862 [1] 462: - - - 4 0.01 - - INFO 2025-06-26 20:21:11,240 calibrate.py _nudge_pos():1868 [1] Points in final series = 53988 INFO 2025-06-26 20:21:11,404 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 43352 INFO 2025-06-26 20:21:11,741 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:12,156 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:12,476 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:12,477 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.108.01/ctd1.nc INFO 2025-06-26 20:21:12,478 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:21:12,479 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 20:21:12,479 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:21:12,865 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:13,185 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:13,187 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.108.01/ctd2.nc INFO 2025-06-26 20:21:13,188 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:21:13,188 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 20:21:13,188 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:21:13,209 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:21:13,754 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:21:13,775 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.108.01 ERROR 2025-06-26 20:21:13,776 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.108.01 INFO 2025-06-26 20:21:13,820 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_cal.nc INFO 2025-06-26 20:21:13,915 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:21:13,921 process.py align():251 [1] Alignment steps for 2014.108.01 INFO 2025-06-26 20:21:13,953 align.py process_cal():139 [1] Processing dorado_2014.108.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.108.01 INFO 2025-06-26 20:21:13,972 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:13,975 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:14,016 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:14,019 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:14,061 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:14,064 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:14,089 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:21:14,089 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:21:14,105 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:14,108 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:14,150 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,153 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,190 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,194 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,231 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,234 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,271 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,274 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,311 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,315 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,351 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,354 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,391 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,395 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,431 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,435 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,474 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,477 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,513 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,517 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,553 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,556 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,593 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,596 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,633 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,636 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,672 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,675 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,712 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,715 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,752 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,756 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,793 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,796 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,832 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,836 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,873 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,876 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,913 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,916 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,955 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,958 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:14,996 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:14,999 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:15,047 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:21:15,082 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:21:15,116 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:21:15,152 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:21:15,188 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:21:15,243 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:21:15,525 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:15,556 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_align.nc INFO 2025-06-26 20:21:15,656 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:21:15,659 process.py resample():273 [1] Resampling steps for 2014.108.01 INFO 2025-06-26 20:21:15,659 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:21:15,689 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_align.nc mission netCDF file INFO 2025-06-26 20:21:15,694 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_align.nc mission netCDF file INFO 2025-06-26 20:21:15,695 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-18T15:06:18.383199744 to 2014-04-18T18:06:15.763528704 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 20:21:15,697 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-18T15:05:35.556133632 to 2014-04-18T18:06:15.643536896 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 20:21:15,698 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-18T15:05:49.705164544 to 2014-04-18T18:06:15.713531904 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 20:21:15,699 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-18T15:05:57.674618368 to 2014-04-18T18:06:15.673534720 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 20:21:15,701 resample.py get_mission_start_end():1145 [1] isus : 2014-04-18T15:06:45.791322112 to 2014-04-18T18:06:14.653604608 (0 days 00:00:01.149921280 before mission_end) INFO 2025-06-26 20:21:15,702 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-18T15:05:29.436518656 to 2014-04-18T18:06:15.123538176 (0 days 00:00:00.679987712 before mission_end) INFO 2025-06-26 20:21:15,703 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-18T15:05:31.706397184 to 2014-04-18T18:06:15.803525888 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:21:15,704 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_align.nc mission netCDF file INFO 2025-06-26 20:21:15,704 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,842 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,866 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,890 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,913 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,934 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,956 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,976 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:15,996 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,015 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,034 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,053 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,072 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,090 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,108 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,127 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,145 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,163 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,184 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,204 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,224 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,244 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,264 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,285 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,305 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,318 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,329 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,340 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,351 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,360 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:16,364 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:21:16,364 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:21:16,742 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:21:16,810 resample.py add_biolume_proxies():633 [1] Zero flow values found: 10847 of 10847 - replaced with 350 ml/s INFO 2025-06-26 20:21:16,810 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:21:16,849 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:21:16,866 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:21:16,882 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:21:16,882 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:21:16,910 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:17,081 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_1S.nc INFO 2025-06-26 20:21:18,861 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:21:30,326 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.108.01/dorado_2014.108.01_1S_Gulper.txt INFO 2025-06-26 20:21:30,327 process.py archive():337 [1] Archiving steps for 2014.108.01 INFO 2025-06-26 20:21:30,327 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:21:30,328 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:21:30,329 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.108.01_1S.nc INFO 2025-06-26 20:21:30,344 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:21:30,345 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.108.01_cal.nc INFO 2025-06-26 20:21:30,421 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:21:30,422 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.108.01_align.nc INFO 2025-06-26 20:21:30,533 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:21:30,552 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,567 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,571 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,585 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,628 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,633 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,651 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,666 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,700 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,717 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.01 done. INFO 2025-06-26 20:21:30,717 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:21:30,718 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.108.01_1S_Gulper.txt INFO 2025-06-26 20:21:30,723 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.108.01/dorado_2014.108.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:21:30,723 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.01/dorado_2014.108.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf