INFO 2025-06-26 05:37:48,364 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2003 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 05:37:48,364 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 7/7/05 - ctdToUse = ctd1 INFO 2025-06-26 05:37:48,364 process.py process_mission():449 [1] Processing BIOLUME mission 2003.228.02 by user docker_user on host 671049448ece INFO 2025-06-26 05:37:48,364 process.py download_process():165 [1] Download and processing steps for 2003.228.02 INFO 2025-06-26 05:37:48,365 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2003/2003228/2003.228.02 INFO 2025-06-26 05:37:48,365 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2003/2003228/2003.228.02 to /data/auv_data/dorado/missionlogs/2003.228.02 INFO 2025-06-26 05:37:50,169 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2003.228.02 INFO 2025-06-26 05:37:50,169 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/ctdDriver.log (5505499 bytes) INFO 2025-06-26 05:37:50,584 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/ctdDriver2.log (5505581 bytes) INFO 2025-06-26 05:37:50,990 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/gps.log (31106 bytes) INFO 2025-06-26 05:37:51,000 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/hydroscatlog.log (3756314 bytes) INFO 2025-06-26 05:37:51,477 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/navigation.log (15325990 bytes) INFO 2025-06-26 05:37:52,540 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/isuslog.log (301173 bytes) INFO 2025-06-26 05:37:52,573 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/parosci.log (3757094 bytes) INFO 2025-06-26 05:37:52,893 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/tailCone.log (3757056 bytes) WARNING 2025-06-26 05:37:52,893 logs2netcdfs.py download_process_logs():795 [1] Failed to parse long_name & units from header in file /data/auv_data/dorado/missionlogs/2003.228.02/tailCone.log INFO 2025-06-26 05:37:52,893 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.228.02/biolume.log (4262352 bytes) INFO 2025-06-26 05:37:53,311 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 05:37:53,533 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.36 seconds WARNING 2025-06-26 05:37:53,533 process.py download_process():196 [1] No lopc.bin file for 2003.228.02 INFO 2025-06-26 05:37:53,533 process.py calibrate():227 [1] Calibration steps for 2003.228.02 INFO 2025-06-26 05:37:53,673 calibrate.py _navigation_process():1524 [1] Converting from Easting/Northing to lat/lon for mission 2003.228.02 INFO 2025-06-26 05:37:53,691 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 05:37:53,693 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 05:37:55,282 calibrate.py _nudge_pos():1806 [1] 186: 0.120 0.0002332 0.0000051 12546 41.82 0.826 0.022 2003-08-16T05:45:37.635669120 INFO 2025-06-26 05:37:55,889 calibrate.py _nudge_pos():1806 [1] 250: 0.090 0.0003845 -0.0001754 12946 43.15 1.320 -0.753 2003-08-16T06:29:50.833912448 INFO 2025-06-26 05:37:56,449 calibrate.py _nudge_pos():1806 [1] 310: 0.070 0.0016707 -0.0009537 13556 45.18 5.481 -3.911 2003-08-16T07:16:02.034072320 INFO 2025-06-26 05:37:56,829 calibrate.py _nudge_pos():1806 [1] 350: 0.070 0.0000499 -0.0000305 15 0.05 158.627 -121.133 2003-08-16T07:16:44.031195264 INFO 2025-06-26 05:37:57,071 calibrate.py _nudge_pos():1806 [1] 376: 0.060 0.0027934 -0.0030180 13646 45.48 9.107 -12.295 2003-08-16T08:02:38.232519680 INFO 2025-06-26 05:37:57,607 calibrate.py _nudge_pos():1806 [1] 432: 0.030 0.0019551 -0.0018867 13586 45.28 6.405 -7.721 2003-08-16T08:48:50.432610816 INFO 2025-06-26 05:37:57,628 calibrate.py _nudge_pos():1806 [1] 434: 0.030 0.0019360 -0.0018691 25 0.08 3590.155 -4329.574 2003-08-16T08:48:56.432199808 INFO 2025-06-26 05:37:58,095 calibrate.py _nudge_pos():1806 [1] 483: 0.150 0.0017770 0.0000382 9480 31.60 8.344 0.224 2003-08-16T09:21:20.429026944 INFO 2025-06-26 05:37:58,309 calibrate.py _nudge_pos():1862 [1] 484: - - - 4 0.01 - - INFO 2025-06-26 05:37:58,309 calibrate.py _nudge_pos():1868 [1] Points in final series = 78188 WARNING 2025-06-26 05:37:58,372 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 05:37:58,936 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:59,504 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:59,961 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:59,963 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2003.228.02/ctd1.nc INFO 2025-06-26 05:37:59,964 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 05:37:59,964 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 05:37:59,964 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 05:38:00,520 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:38:00,979 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:38:00,981 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2003.228.02/ctd2.nc INFO 2025-06-26 05:38:00,982 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 05:38:00,983 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 05:38:00,983 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 05:38:01,008 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 05:38:01,750 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 540 27900 27901 27902 27903 27904 27905 27906 27907 27908 27909 27910 27911 27912 27913 27914 27915 27916 27917 27918 27919 27920 27921 27922 27923 27924 27925 27926 27927 27928 27929 27930 27931 68940 213360 234900 237180 237480 238500 239400 240780 241440 241560 248340 248520 248940 249120 250560 251280 252840 258660 260760 261120 264960 265860 270480 276000 301320 304020 305700 364680 395760 397860 400200 411300 427560 439200 451440 462720 488460 504840 612120 629100 691620 701160 706440 707460 708300 708420 708540 710400 710640 712020 712380 712980 713160 713940 715380 717120 721620 742560 762660 762840 769980 772380 772980 779940 793380 793560 795780 796980 804840 838920 839280 847920 859560 878100 937860] INFO 2025-06-26 05:38:01,885 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 05:38:01,890 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 05:38:01,891 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2003.228.02 ERROR 2025-06-26 05:38:01,891 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2003.228.02 ERROR 2025-06-26 05:38:01,891 calibrate.py process_logs():3542 [1] Error processing tailcone: tailcone has no orig_data - likely a missing or zero-sized .log file in missionlogs/2003.228.02 INFO 2025-06-26 05:38:01,892 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_cal.nc INFO 2025-06-26 05:38:01,965 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_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, 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, time INFO 2025-06-26 05:38:01,969 process.py align():251 [1] Alignment steps for 2003.228.02 INFO 2025-06-26 05:38:01,994 align.py process_cal():139 [1] Processing dorado_2003.228.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2003.228.02 INFO 2025-06-26 05:38:02,020 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:38:02,023 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:38:02,084 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:38:02,088 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:38:02,147 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:38:02,151 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:38:02,187 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 05:38:02,187 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 05:38:02,211 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:38:02,215 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:38:02,273 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:38:02,277 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,329 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:38:02,333 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,385 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:38:02,389 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,442 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,446 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,498 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,502 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,553 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,557 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,609 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,612 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,664 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,667 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,719 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,723 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,774 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,778 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,829 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,833 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,885 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,888 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,939 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,943 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:02,995 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:02,999 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:03,052 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:03,056 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:03,109 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:03,114 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:03,166 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:03,170 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:03,222 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:03,226 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:03,278 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:03,282 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:03,333 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.228.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:38:03,336 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:38:03,393 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.60 INFO 2025-06-26 05:38:03,429 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.60 INFO 2025-06-26 05:38:03,466 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.60 INFO 2025-06-26 05:38:03,505 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 05:38:03,521 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_align.nc INFO 2025-06-26 05:38:03,584 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_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, 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 INFO 2025-06-26 05:38:03,586 process.py resample():273 [1] Resampling steps for 2003.228.02 INFO 2025-06-26 05:38:03,587 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 05:38:03,609 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_align.nc mission netCDF file INFO 2025-06-26 05:38:03,614 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_align.nc mission netCDF file INFO 2025-06-26 05:38:03,615 resample.py get_mission_start_end():1145 [1] navigation: 2003-08-16T05:01:05.838699648 to 2003-08-16T09:21:43.237464576 (0 days 00:00:00.049996416 before mission_end) INFO 2025-06-26 05:38:03,617 resample.py get_mission_start_end():1145 [1] hs2 : 2003-08-16T05:00:47.779936768 to 2003-08-16T09:21:43.287460992 (0 days 00:00:00 before mission_end) INFO 2025-06-26 05:38:03,618 resample.py get_mission_start_end():1145 [1] ctd1 : 2003-08-16T05:01:03.798839424 to 2003-08-16T09:21:43.177468672 (0 days 00:00:00.109992320 before mission_end) INFO 2025-06-26 05:38:03,620 resample.py get_mission_start_end():1145 [1] ctd2 : 2003-08-16T05:01:03.558855936 to 2003-08-16T09:21:43.167469312 (0 days 00:00:00.119991680 before mission_end) INFO 2025-06-26 05:38:03,621 resample.py get_mission_start_end():1145 [1] isus : 2003-08-16T05:01:59.785004160 to 2003-08-16T09:21:42.057545344 (0 days 00:00:01.229915648 before mission_end) INFO 2025-06-26 05:38:03,622 resample.py get_mission_start_end():1145 [1] biolume : 2003-08-16T05:00:43.050226560 to 2003-08-16T09:21:42.717465856 (0 days 00:00:00.569995136 before mission_end) INFO 2025-06-26 05:38:03,623 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_align.nc mission netCDF file INFO 2025-06-26 05:38:03,623 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:03,801 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:03,832 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:03,863 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:03,893 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:03,921 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:03,948 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:03,975 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,002 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,028 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,052 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,077 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,101 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,129 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,158 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,183 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,207 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,234 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,260 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,287 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,312 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,338 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,363 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,376 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,389 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,401 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,414 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 05:38:04,592 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_1S.nc INFO 2025-06-26 05:38:05,823 create_products.py gulper_odv():401 [1] No gulper times found for 2003.228.02 INFO 2025-06-26 05:38:05,823 process.py archive():337 [1] Archiving steps for 2003.228.02 INFO 2025-06-26 05:38:05,823 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02, BASE_PATH = /data/auv_data INFO 2025-06-26 05:38:05,824 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02 files to /Volumes/AUVCTD/surveys/2003/netcdf INFO 2025-06-26 05:38:05,825 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2003/netcdf/dorado_2003.228.02_1S.nc INFO 2025-06-26 05:38:05,840 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_1S.nc /Volumes/AUVCTD/surveys/2003/netcdf done. INFO 2025-06-26 05:38:05,841 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2003/netcdf/dorado_2003.228.02_cal.nc INFO 2025-06-26 05:38:05,903 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_cal.nc /Volumes/AUVCTD/surveys/2003/netcdf done. INFO 2025-06-26 05:38:05,904 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2003/netcdf/dorado_2003.228.02_align.nc INFO 2025-06-26 05:38:05,963 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_align.nc /Volumes/AUVCTD/surveys/2003/netcdf done. INFO 2025-06-26 05:38:05,985 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,006 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,010 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,025 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,072 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,078 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,093 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,142 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003228/2003.228.02 done. INFO 2025-06-26 05:38:06,142 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 05:38:06,142 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.228.02/dorado_2003.228.02_processing.log /Volumes/AUVCTD/surveys/2003/netcdf