INFO 2025-06-26 13:55:14,978 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 13:55:14,978 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Autonomy group missions over canyon axis between M0 & M1 (gulper trips in nice layers) - ctdToUse = ctd1 INFO 2025-06-26 13:55:14,978 process.py process_mission():449 [1] Processing AUVCTD mission 2008.010.08 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:55:14,978 process.py download_process():165 [1] Download and processing steps for 2008.010.08 INFO 2025-06-26 13:55:14,979 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008010/2008.010.08 INFO 2025-06-26 13:55:14,979 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008010/2008.010.08 to /data/auv_data/dorado/missionlogs/2008.010.08 INFO 2025-06-26 13:55:17,506 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.010.08 INFO 2025-06-26 13:55:17,507 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/ctdDriver.log (1863174 bytes) INFO 2025-06-26 13:55:17,645 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/ctdDriver2.log (1862975 bytes) INFO 2025-06-26 13:55:17,810 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/gps.log (82796 bytes) INFO 2025-06-26 13:55:17,826 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/hydroscatlog.log (1169594 bytes) INFO 2025-06-26 13:55:17,971 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/navigation.log (5719350 bytes) INFO 2025-06-26 13:55:18,420 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/isuslog.log (120085 bytes) INFO 2025-06-26 13:55:18,449 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/parosci.log (1915622 bytes) INFO 2025-06-26 13:55:18,617 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/tailCone.log (249067 bytes) INFO 2025-06-26 13:55:18,654 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.08/biolume.log (1329948 bytes) INFO 2025-06-26 13:55:18,782 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:55:18,859 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.35 seconds WARNING 2025-06-26 13:55:18,860 process.py download_process():196 [1] No lopc.bin file for 2008.010.08 INFO 2025-06-26 13:55:18,860 process.py calibrate():227 [1] Calibration steps for 2008.010.08 INFO 2025-06-26 13:55:18,945 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 13:55:18,947 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:55:19,406 calibrate.py _nudge_pos():1806 [1] 76: 0.070 0.0007241 -0.0002763 1525 5.08 21.152 -10.077 2008-01-10T20:23:05.740980992 INFO 2025-06-26 13:55:20,741 calibrate.py _nudge_pos():1806 [1] 220: 0.070 0.0035562 -0.0002626 7475 24.91 21.188 -1.954 2008-01-10T20:50:23.738770432 INFO 2025-06-26 13:55:20,752 calibrate.py _nudge_pos():1806 [1] 221: 0.080 -0.0000095 0.0000527 165 0.55 -2.576 17.872 2008-01-10T20:50:56.736509952 INFO 2025-06-26 13:55:21,808 calibrate.py _nudge_pos():1806 [1] 319: 0.070 -0.0009052 0.0005571 9340 31.13 -4.315 3.316 2008-01-10T21:23:41.741897728 INFO 2025-06-26 13:55:21,837 calibrate.py _nudge_pos():1806 [1] 322: 0.080 0.0000881 0.0000281 225 0.75 17.503 6.982 2008-01-10T21:24:28.738678528 INFO 2025-06-26 13:55:29,476 calibrate.py _nudge_pos():1862 [1] 1105: - - - 2 0.00 - - INFO 2025-06-26 13:55:29,476 calibrate.py _nudge_pos():1868 [1] Points in final series = 24226 WARNING 2025-06-26 13:55:29,512 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 13:55:29,706 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:29,914 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:55:30,068 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:55:30,070 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.010.08/ctd1.nc INFO 2025-06-26 13:55:30,071 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:55:30,072 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 13:55:30,072 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:55:30,259 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:30,411 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:30,413 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.010.08/ctd2.nc INFO 2025-06-26 13:55:30,414 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 13:55:30,415 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 13:55:30,415 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:55:30,429 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:55:30,641 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 120 121 180 600 24060 24061 24062 24063 30480 30481 30482 30600 30601 30602 37260 52620 62340 127920 128220 143340 143341 143342 143580 143581 143582 172800 172801 172802 241740 241741 241742 243180 251880 251881 252600 252601 260580 260581 260582 262020 262021 262022 262740 262741 262742 264180 264181 264182 264900 264901 264902 265620 265621 265622 266400 266401 266402 266403 274560 274561 274562 274563 276000 276001 276002 276003 278160 278161 278162 278163 284940 284941 284942 288300 288301 288302 288303 288304 288305 290460 290461 290462 290463 290464 290465 291180 291181 291182 291183 291184 291185 291900 291901 291902 291903 291904 291905] INFO 2025-06-26 13:55:30,687 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:55:30,693 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 13:55:30,694 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.010.08 ERROR 2025-06-26 13:55:30,694 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.010.08 INFO 2025-06-26 13:55:30,701 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_cal.nc INFO 2025-06-26 13:55:30,754 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, 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_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 13:55:30,758 process.py align():251 [1] Alignment steps for 2008.010.08 INFO 2025-06-26 13:55:30,782 align.py process_cal():139 [1] Processing dorado_2008.010.08_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.010.08 INFO 2025-06-26 13:55:30,793 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:30,795 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:30,819 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:30,822 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:30,845 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:30,848 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:30,861 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:55:30,861 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:55:30,871 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:30,873 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:30,895 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:30,897 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:30,919 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:30,921 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:30,942 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:30,945 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:30,967 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:30,969 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:30,991 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:30,993 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,015 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,018 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,039 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,042 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,063 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,066 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,087 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,089 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,110 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,113 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,134 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,137 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,158 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,160 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,181 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,184 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,205 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,207 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,229 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,231 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,253 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,255 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,277 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,280 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,302 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,305 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,327 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,330 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,352 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,355 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,377 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,379 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,401 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:31,403 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:31,430 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:31,452 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:31,474 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:31,497 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:55:31,520 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.06 INFO 2025-06-26 13:55:31,533 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_align.nc INFO 2025-06-26 13:55:31,585 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, 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_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 13:55:31,587 process.py resample():273 [1] Resampling steps for 2008.010.08 INFO 2025-06-26 13:55:31,587 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:55:31,610 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_align.nc mission netCDF file INFO 2025-06-26 13:55:31,615 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_align.nc mission netCDF file INFO 2025-06-26 13:55:31,616 resample.py get_mission_start_end():1145 [1] navigation: 2008-01-10T20:17:19.244717568 to 2008-01-10T21:38:04.142819328 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:55:31,617 resample.py get_mission_start_end():1145 [1] hs2 : 2008-01-10T20:16:52.646539776 to 2008-01-10T21:38:04.052825344 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 13:55:31,618 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-01-10T20:17:13.745094400 to 2008-01-10T21:38:04.132820224 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 13:55:31,620 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-01-10T20:17:13.935081216 to 2008-01-10T21:38:04.062824704 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 13:55:31,621 resample.py get_mission_start_end():1145 [1] isus : 2008-01-10T20:18:00.461894144 to 2008-01-10T21:38:03.182885120 (0 days 00:00:00.959934208 before mission_end) INFO 2025-06-26 13:55:31,622 resample.py get_mission_start_end():1145 [1] biolume : 2008-01-10T20:16:45.496995328 to 2008-01-10T21:38:02.842874112 (0 days 00:00:01.299945216 before mission_end) INFO 2025-06-26 13:55:31,624 resample.py get_mission_start_end():1145 [1] tailcone : 2008-01-10T20:16:49.066784768 to 2008-01-10T21:38:03.972830976 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 13:55:31,624 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_align.nc mission netCDF file INFO 2025-06-26 13:55:31,625 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,698 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,714 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,729 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,743 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,758 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,772 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,785 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,798 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,811 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,823 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,835 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,847 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,860 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,872 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,884 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,897 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,909 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,923 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,937 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,951 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,965 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,979 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:31,992 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:32,006 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:32,017 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:32,027 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:32,037 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:32,048 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:32,060 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:32,184 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_1S.nc INFO 2025-06-26 13:55:33,719 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:55:38,050 create_products.py gulper_odv():522 [1] Wrote 4 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.010.08/dorado_2008.010.08_1S_Gulper.txt INFO 2025-06-26 13:55:38,050 process.py archive():337 [1] Archiving steps for 2008.010.08 INFO 2025-06-26 13:55:38,050 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08, BASE_PATH = /data/auv_data INFO 2025-06-26 13:55:38,050 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 13:55:38,051 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.08_1S.nc INFO 2025-06-26 13:55:38,062 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:38,063 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.08_cal.nc INFO 2025-06-26 13:55:38,088 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:38,089 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.08_align.nc INFO 2025-06-26 13:55:38,113 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:38,125 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,136 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,140 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,148 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,168 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,173 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,184 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,190 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,209 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.08 done. INFO 2025-06-26 13:55:38,209 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:55:38,210 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.010.08_1S_Gulper.txt INFO 2025-06-26 13:55:38,215 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.010.08/dorado_2008.010.08_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 13:55:38,216 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.08/dorado_2008.010.08_processing.log /Volumes/AUVCTD/surveys/2008/netcdf