INFO 2025-06-26 13:58:28,622 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 13:58:28,622 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Autonomy TREX mission - ctdToUse = ctd1 INFO 2025-06-26 13:58:28,623 process.py process_mission():449 [1] Processing AUVCTD mission 2008.133.04 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:58:28,623 process.py download_process():165 [1] Download and processing steps for 2008.133.04 INFO 2025-06-26 13:58:28,623 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008133/2008.133.04 INFO 2025-06-26 13:58:28,623 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008133/2008.133.04 to /data/auv_data/dorado/missionlogs/2008.133.04 INFO 2025-06-26 13:58:31,297 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.133.04 INFO 2025-06-26 13:58:31,298 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/ctdDriver.log (3851814 bytes) INFO 2025-06-26 13:58:31,575 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/ctdDriver2.log (3851519 bytes) INFO 2025-06-26 13:58:31,855 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/gps.log (48668 bytes) INFO 2025-06-26 13:58:31,868 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/hydroscatlog.log (2412194 bytes) INFO 2025-06-26 13:58:32,153 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.133.04/hydroscatlog.log: [39854 39855 39856] INFO 2025-06-26 13:58:32,160 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/navigation.log (11831514 bytes) INFO 2025-06-26 13:58:33,024 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/isuslog.log (249397 bytes) INFO 2025-06-26 13:58:33,053 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/parosci.log (3948134 bytes) INFO 2025-06-26 13:58:33,393 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/tailCone.log (510091 bytes) INFO 2025-06-26 13:58:33,461 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.133.04/biolume.log (2738908 bytes) INFO 2025-06-26 13:58:33,718 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:58:33,866 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.57 seconds WARNING 2025-06-26 13:58:33,867 process.py download_process():196 [1] No lopc.bin file for 2008.133.04 INFO 2025-06-26 13:58:33,867 process.py calibrate():227 [1] Calibration steps for 2008.133.04 INFO 2025-06-26 13:58:33,993 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 13:58:33,995 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:58:34,521 calibrate.py _nudge_pos():1806 [1] 79: 0.190 0.0011116 0.0005362 3060 10.20 16.164 9.744 2008-05-12T16:08:35.990763520 INFO 2025-06-26 13:58:34,531 calibrate.py _nudge_pos():1806 [1] 80: 0.190 -0.0000365 -0.0000128 20 0.06 -85.375 -37.522 2008-05-12T16:08:39.990489600 INFO 2025-06-26 13:58:36,302 calibrate.py _nudge_pos():1806 [1] 268: 0.190 0.0074519 0.0004251 19415 64.71 17.083 1.217 2008-05-12T17:16:29.991675392 INFO 2025-06-26 13:58:36,313 calibrate.py _nudge_pos():1806 [1] 269: 0.200 -0.0000329 -0.0000237 140 0.46 -10.538 -9.462 2008-05-12T17:16:57.989757184 INFO 2025-06-26 13:58:37,739 calibrate.py _nudge_pos():1806 [1] 420: 0.200 -0.0001862 -0.0004995 24339 81.13 -0.340 -1.141 2008-05-12T18:40:35.996000256 INFO 2025-06-26 13:58:40,033 calibrate.py _nudge_pos():1862 [1] 635: - - - 3 0.01 - - INFO 2025-06-26 13:58:40,033 calibrate.py _nudge_pos():1868 [1] Points in final series = 49814 WARNING 2025-06-26 13:58:40,101 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 13:58:45,540 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: -3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:58:45,936 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:58:46,234 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:58:46,236 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.133.04/ctd1.nc INFO 2025-06-26 13:58:46,237 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:58:46,238 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 13:58:46,238 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:58:46,600 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:58:46,899 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:58:46,901 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.133.04/ctd2.nc INFO 2025-06-26 13:58:46,902 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 13:58:46,903 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 13:58:46,903 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:58:46,923 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:58:47,428 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 240 241 900 901 902 903 6540 6541 6542 6543 6544 6545 16800 16801 16802 20760 20761 20762 35700 49080 56880 56881 56882 56883 56884 102240 156480 156481 156482 174480 213540 213541 213542 213543 213544 245220 328740 360960 360961 360962 360963 586320 586321 586322 599340] INFO 2025-06-26 13:58:47,517 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -9 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:58:47,523 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 13:58:47,523 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.133.04 ERROR 2025-06-26 13:58:47,523 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.133.04 INFO 2025-06-26 13:58:47,535 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_cal.nc INFO 2025-06-26 13:58:47,605 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 13:58:47,609 process.py align():251 [1] Alignment steps for 2008.133.04 INFO 2025-06-26 13:58:47,635 align.py process_cal():139 [1] Processing dorado_2008.133.04_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.133.04 INFO 2025-06-26 13:58:47,652 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:58:47,655 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:58:47,695 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:58:47,698 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:58:47,737 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:58:47,741 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:58:47,763 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:58:47,763 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:58:47,778 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:58:47,781 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:58:47,821 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:47,825 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:47,869 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:47,873 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:47,910 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:47,913 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:47,948 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:47,951 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:47,987 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:47,990 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,025 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,029 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,064 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,067 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,101 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,104 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,139 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,142 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,176 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,180 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,215 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,219 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,253 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,256 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,291 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,295 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,329 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,332 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,368 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,371 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,405 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,409 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,445 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,448 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,482 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,485 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,520 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,524 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,558 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,562 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,597 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,601 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,635 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.133.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:58:48,638 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:58:48,680 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:58:48,711 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:58:48,743 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:58:48,776 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:58:48,809 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.06 INFO 2025-06-26 13:58:48,825 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_align.nc INFO 2025-06-26 13:58:48,886 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 13:58:48,888 process.py resample():273 [1] Resampling steps for 2008.133.04 INFO 2025-06-26 13:58:48,888 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:58:48,913 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_align.nc mission netCDF file INFO 2025-06-26 13:58:48,918 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_align.nc mission netCDF file INFO 2025-06-26 13:58:48,919 resample.py get_mission_start_end():1145 [1] navigation: 2008-05-12T15:57:35.086038528 to 2008-05-12T18:44:39.789299200 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 13:58:48,920 resample.py get_mission_start_end():1145 [1] hs2 : 2008-05-12T15:57:08.497859840 to 2008-05-12T18:44:39.809297920 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 13:58:48,922 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-05-12T15:57:30.786333184 to 2008-05-12T18:44:39.829296640 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:58:48,923 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-05-12T15:57:30.776333824 to 2008-05-12T18:44:39.789299200 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 13:58:48,924 resample.py get_mission_start_end():1145 [1] isus : 2008-05-12T15:58:18.553060864 to 2008-05-12T18:44:39.829296640 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:58:48,926 resample.py get_mission_start_end():1145 [1] biolume : 2008-05-12T15:57:02.108263424 to 2008-05-12T18:44:38.959321856 (0 days 00:00:00.869974784 before mission_end) INFO 2025-06-26 13:58:48,927 resample.py get_mission_start_end():1145 [1] tailcone : 2008-05-12T15:57:08.407866112 to 2008-05-12T18:44:39.309332224 (0 days 00:00:00.519964416 before mission_end) INFO 2025-06-26 13:58:48,928 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_align.nc mission netCDF file INFO 2025-06-26 13:58:48,928 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,058 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,082 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,105 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,128 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,150 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,170 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,192 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,212 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,231 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,249 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,268 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,287 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,306 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,325 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,343 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,362 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,381 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,402 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,422 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,442 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,461 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,480 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,500 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,519 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,532 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,543 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,554 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,567 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,579 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:58:49,733 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_1S.nc INFO 2025-06-26 13:58:51,615 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:59:00,123 create_products.py gulper_odv():522 [1] Wrote 8 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.133.04/dorado_2008.133.04_1S_Gulper.txt INFO 2025-06-26 13:59:00,123 process.py archive():337 [1] Archiving steps for 2008.133.04 INFO 2025-06-26 13:59:00,123 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04, BASE_PATH = /data/auv_data INFO 2025-06-26 13:59:00,123 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 13:59:00,124 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.133.04_1S.nc INFO 2025-06-26 13:59:00,138 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:59:00,139 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.133.04_cal.nc INFO 2025-06-26 13:59:00,185 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:59:00,186 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.133.04_align.nc INFO 2025-06-26 13:59:00,227 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:59:00,244 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,259 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,264 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,275 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,309 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,315 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,329 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,336 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,366 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008133/2008.133.04 done. INFO 2025-06-26 13:59:00,366 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:59:00,368 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.133.04_1S_Gulper.txt INFO 2025-06-26 13:59:00,373 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.133.04/dorado_2008.133.04_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 13:59:00,373 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.133.04/dorado_2008.133.04_processing.log /Volumes/AUVCTD/surveys/2008/netcdf