INFO 2025-06-26 10:39:43,568 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 10:39:43,568 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ctdToUse = ctd1 INFO 2025-06-26 10:39:43,568 process.py process_mission():449 [1] Processing AUVCTD mission 2005.159.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:39:43,568 process.py download_process():165 [1] Download and processing steps for 2005.159.00 INFO 2025-06-26 10:39:43,569 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005159/2005.159.00 INFO 2025-06-26 10:39:43,569 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005159/2005.159.00 to /data/auv_data/dorado/missionlogs/2005.159.00 INFO 2025-06-26 10:39:44,190 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.159.00 INFO 2025-06-26 10:39:44,190 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/ctdDriver.log (6489427 bytes) INFO 2025-06-26 10:39:44,655 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/ctdDriver2.log (6492501 bytes) INFO 2025-06-26 10:39:45,122 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.159.00/ctdDriver2.log: [11294] INFO 2025-06-26 10:39:45,143 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/gps.log (50180 bytes) INFO 2025-06-26 10:39:45,157 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/hydroscatlog.log (4429454 bytes) INFO 2025-06-26 10:39:45,670 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.159.00/hydroscatlog.log: [69943] INFO 2025-06-26 10:39:45,682 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/navigation.log (21756494 bytes) INFO 2025-06-26 10:39:47,248 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/isuslog.log (398357 bytes) INFO 2025-06-26 10:39:47,291 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/parosci.log (9496262 bytes) INFO 2025-06-26 10:39:48,061 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.159.00/parosci.log: [1381 1382] INFO 2025-06-26 10:39:48,089 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/tailCone.log (4430539 bytes) INFO 2025-06-26 10:39:48,632 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.159.00/biolume.log (5025612 bytes) INFO 2025-06-26 10:39:49,110 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:39:49,367 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.18 seconds WARNING 2025-06-26 10:39:49,367 process.py download_process():196 [1] No lopc.bin file for 2005.159.00 INFO 2025-06-26 10:39:49,368 process.py calibrate():227 [1] Calibration steps for 2005.159.00 INFO 2025-06-26 10:39:49,533 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 10:39:49,535 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:39:51,213 calibrate.py _nudge_pos():1806 [1] 193: 0.090 0.0044178 -0.0023497 12014 40.06 16.378 -10.868 2005-06-08T17:32:00.305688832 INFO 2025-06-26 10:39:51,892 calibrate.py _nudge_pos():1806 [1] 264: 0.090 0.0064437 -0.0036622 12063 40.23 23.787 -16.868 2005-06-08T18:13:24.305523200 INFO 2025-06-26 10:39:52,389 calibrate.py _nudge_pos():1806 [1] 316: 0.090 0.0049134 -0.0028042 12043 40.15 18.174 -12.943 2005-06-08T18:54:24.307001600 INFO 2025-06-26 10:39:53,110 calibrate.py _nudge_pos():1806 [1] 391: 0.090 0.0039606 -0.0026641 12020 40.06 14.679 -12.322 2005-06-08T19:35:42.307246976 INFO 2025-06-26 10:39:53,771 calibrate.py _nudge_pos():1806 [1] 460: 0.090 0.0034823 -0.0022432 11987 39.96 12.937 -10.401 2005-06-08T20:16:48.308314368 INFO 2025-06-26 10:39:54,443 calibrate.py _nudge_pos():1806 [1] 529: 0.090 0.0055916 -0.0039205 12108 40.36 20.566 -17.998 2005-06-08T20:58:18.307737600 INFO 2025-06-26 10:39:55,120 calibrate.py _nudge_pos():1806 [1] 599: 0.090 0.0026348 -0.0016271 12369 41.25 9.482 -7.310 2005-06-08T21:40:42.303462016 INFO 2025-06-26 10:39:55,805 calibrate.py _nudge_pos():1806 [1] 669: 0.090 0.0000622 0.0001914 4305 14.35 0.644 2.472 2005-06-08T21:56:12.309752192 INFO 2025-06-26 10:39:55,956 calibrate.py _nudge_pos():1862 [1] 663: - - - 1 0.00 - - INFO 2025-06-26 10:39:55,957 calibrate.py _nudge_pos():1868 [1] Points in final series = 92180 WARNING 2025-06-26 10:39:59,132 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 10:40:08,888 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:40:09,603 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:40:10,161 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:40:10,163 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.159.00/ctd1.nc INFO 2025-06-26 10:40:10,164 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 10:40:10,164 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 10:40:10,164 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:40:14,235 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:40:14,802 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:40:14,804 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.159.00/ctd2.nc INFO 2025-06-26 10:40:14,805 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 10:40:14,806 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 10:40:14,806 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:40:14,836 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:40:15,697 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [403920 488100 750480] INFO 2025-06-26 10:40:15,863 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:40:15,869 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 10:40:15,869 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.159.00 ERROR 2025-06-26 10:40:15,870 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.159.00 INFO 2025-06-26 10:40:15,942 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_cal.nc INFO 2025-06-26 10:40:18,328 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, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 10:40:18,332 process.py align():251 [1] Alignment steps for 2005.159.00 INFO 2025-06-26 10:40:18,360 align.py process_cal():139 [1] Processing dorado_2005.159.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.159.00 INFO 2025-06-26 10:40:18,388 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:40:18,392 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:40:18,464 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:40:18,469 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:40:18,537 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:40:18,544 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:40:18,588 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:40:18,589 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:40:18,617 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:40:18,622 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:40:18,688 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:40:18,692 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:18,751 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:40:18,755 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:18,814 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:40:18,818 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:18,878 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:18,882 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:18,943 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:18,947 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,007 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,011 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,070 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,074 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,131 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,135 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,193 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,197 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,256 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,261 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,319 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,323 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,381 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,385 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,443 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,447 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,507 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,511 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,570 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,574 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,634 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,638 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,699 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,703 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,762 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,766 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,825 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,830 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,888 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.159.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:40:19,892 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:40:19,969 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:40:20,028 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:40:20,081 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:40:20,142 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:40:20,200 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:40:20,248 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_align.nc INFO 2025-06-26 10:40:20,328 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, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 10:40:20,330 process.py resample():273 [1] Resampling steps for 2005.159.00 INFO 2025-06-26 10:40:20,330 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:40:20,357 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_align.nc mission netCDF file INFO 2025-06-26 10:40:20,362 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_align.nc mission netCDF file INFO 2025-06-26 10:40:20,364 resample.py get_mission_start_end():1145 [1] navigation: 2005-06-08T16:49:06.522005120 to 2005-06-08T21:56:27.508710912 (0 days 00:00:00.069995392 before mission_end) INFO 2025-06-26 10:40:20,365 resample.py get_mission_start_end():1145 [1] hs2 : 2005-06-08T16:48:48.503239424 to 2005-06-08T21:56:27.528709632 (0 days 00:00:00.049996672 before mission_end) INFO 2025-06-26 10:40:20,367 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-06-08T16:49:11.061694208 to 2005-06-08T21:56:27.348721920 (0 days 00:00:00.229984384 before mission_end) INFO 2025-06-26 10:40:20,369 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-06-08T16:49:02.792260608 to 2005-06-08T21:56:27.338722688 (0 days 00:00:00.239983616 before mission_end) INFO 2025-06-26 10:40:20,370 resample.py get_mission_start_end():1145 [1] isus : 2005-06-08T16:50:00.538304768 to 2005-06-08T21:56:26.268795904 (0 days 00:00:01.309910400 before mission_end) INFO 2025-06-26 10:40:20,371 resample.py get_mission_start_end():1145 [1] biolume : 2005-06-08T16:48:43.723532672 to 2005-06-08T21:56:26.728730240 (0 days 00:00:00.849976064 before mission_end) INFO 2025-06-26 10:40:20,373 resample.py get_mission_start_end():1145 [1] tailcone : 2005-06-08T16:48:44.383521536 to 2005-06-08T21:56:27.578706304 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:40:20,374 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_align.nc mission netCDF file INFO 2025-06-26 10:40:20,374 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,592 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,629 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,665 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,701 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,733 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,764 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,795 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,826 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,854 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,883 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,911 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,940 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,969 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:20,998 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,028 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,057 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,087 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,119 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,149 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,178 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,207 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,236 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,252 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,265 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,277 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,292 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,325 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:40:21,522 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_1S.nc INFO 2025-06-26 10:40:22,568 create_products.py gulper_odv():401 [1] No gulper times found for 2005.159.00 INFO 2025-06-26 10:40:22,568 process.py archive():337 [1] Archiving steps for 2005.159.00 INFO 2025-06-26 10:40:22,568 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00, BASE_PATH = /data/auv_data INFO 2025-06-26 10:40:22,568 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:40:22,569 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.159.00_1S.nc INFO 2025-06-26 10:40:22,586 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:40:22,587 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.159.00_cal.nc INFO 2025-06-26 10:40:22,674 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:40:22,674 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.159.00_align.nc INFO 2025-06-26 10:40:22,762 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:40:22,787 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:22,809 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:22,813 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:22,829 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:22,892 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:22,898 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:22,928 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:22,948 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:23,001 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005159/2005.159.00 done. INFO 2025-06-26 10:40:23,001 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:40:23,001 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.159.00/dorado_2005.159.00_processing.log /Volumes/AUVCTD/surveys/2005/netcdf