INFO 2025-06-26 05:55:16,424 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 05:55:16,424 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 8/16/05 - ctdToUse = ctd1 INFO 2025-06-26 05:55:16,424 process.py process_mission():449 [1] Processing OCCO mission 2004.239.01 by user docker_user on host 671049448ece INFO 2025-06-26 05:55:16,424 process.py download_process():165 [1] Download and processing steps for 2004.239.01 INFO 2025-06-26 05:55:16,424 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004239/2004.239.01 INFO 2025-06-26 05:55:16,424 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004239/2004.239.01 to /data/auv_data/dorado/missionlogs/2004.239.01 INFO 2025-06-26 05:55:21,802 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.239.01 INFO 2025-06-26 05:55:21,802 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/ctdDriver.log (5763339 bytes) INFO 2025-06-26 05:55:22,218 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/ctdDriver2.log (5763333 bytes) INFO 2025-06-26 05:55:22,671 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/gps.log (33332 bytes) INFO 2025-06-26 05:55:22,683 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/hydroscatlog.log (3929954 bytes) INFO 2025-06-26 05:55:23,194 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.239.01/hydroscatlog.log: [5] INFO 2025-06-26 05:55:23,205 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/navigation.log (12760495 bytes) INFO 2025-06-26 05:55:24,188 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/isuslog.log (591356 bytes) INFO 2025-06-26 05:55:24,249 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/parosci.log (3931478 bytes) INFO 2025-06-26 05:55:24,604 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/tailCone.log (3931483 bytes) INFO 2025-06-26 05:55:25,113 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.239.01/biolume.log (4459308 bytes) INFO 2025-06-26 05:55:25,592 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 05:55:25,832 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.03 seconds WARNING 2025-06-26 05:55:25,833 process.py download_process():196 [1] No lopc.bin file for 2004.239.01 INFO 2025-06-26 05:55:25,834 process.py calibrate():227 [1] Calibration steps for 2004.239.01 INFO 2025-06-26 05:55:26,005 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 05:55:26,008 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 05:55:27,416 calibrate.py _nudge_pos():1806 [1] 166: 0.100 -0.0010085 0.0001750 8015 26.71 -5.592 1.214 2004-08-26T16:56:37.145371008 INFO 2025-06-26 05:55:27,856 calibrate.py _nudge_pos():1806 [1] 213: 0.100 -0.0014260 0.0004022 11410 38.03 -5.556 1.960 2004-08-26T17:35:25.145892096 INFO 2025-06-26 05:55:28,285 calibrate.py _nudge_pos():1806 [1] 258: 0.090 -0.0014769 0.0005493 11660 38.86 -5.633 2.619 2004-08-26T18:15:01.153124352 INFO 2025-06-26 05:55:28,671 calibrate.py _nudge_pos():1806 [1] 297: 0.100 -0.0015286 0.0005545 11690 38.96 -5.818 2.637 2004-08-26T18:54:37.150357504 INFO 2025-06-26 05:55:29,127 calibrate.py _nudge_pos():1806 [1] 345: 0.110 -0.0012784 -0.0000634 11642 38.81 -4.886 -0.303 2004-08-26T19:34:13.147590400 INFO 2025-06-26 05:55:29,139 calibrate.py _nudge_pos():1806 [1] 346: 0.110 -0.0012227 -0.0001038 80 0.26 -688.870 -73.028 2004-08-26T19:34:29.146494336 INFO 2025-06-26 05:55:29,539 calibrate.py _nudge_pos():1806 [1] 388: 0.110 -0.0004089 -0.0016611 12105 40.35 -1.504 -7.629 2004-08-26T20:15:31.147835776 INFO 2025-06-26 05:55:29,690 calibrate.py _nudge_pos():1806 [1] 404: 0.100 0.0000621 -0.0000697 120 0.40 23.225 -32.568 2004-08-26T20:16:10.145164288 INFO 2025-06-26 05:55:30,132 calibrate.py _nudge_pos():1862 [1] 428: - - - 12972 43.25 - - INFO 2025-06-26 05:55:30,132 calibrate.py _nudge_pos():1868 [1] Points in final series = 81790 WARNING 2025-06-26 05:55:30,198 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 05:55:38,767 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:55:39,361 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 10 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:55:39,836 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 10 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:55:39,838 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.239.01/ctd1.nc INFO 2025-06-26 05:55:39,840 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 05:55:39,840 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 05:55:39,840 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 05:55:40,424 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 10 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:55:40,907 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 10 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:55:40,910 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.239.01/ctd2.nc INFO 2025-06-26 05:55:40,911 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 05:55:40,912 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 05:55:40,912 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 05:55:40,945 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 05:55:41,859 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 05:55:41,866 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 05:55:41,867 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.239.01 ERROR 2025-06-26 05:55:41,867 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.239.01 INFO 2025-06-26 05:55:41,936 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_cal.nc INFO 2025-06-26 05:55:42,018 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 05:55:42,024 process.py align():251 [1] Alignment steps for 2004.239.01 INFO 2025-06-26 05:55:42,052 align.py process_cal():139 [1] Processing dorado_2004.239.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.239.01 INFO 2025-06-26 05:55:42,078 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:55:42,082 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:55:42,146 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:55:42,151 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:55:42,212 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:55:42,216 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:55:42,252 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 05:55:42,253 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 05:55:42,277 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:55:42,282 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:55:42,341 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:55:42,346 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,401 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:55:42,405 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,459 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:55:42,464 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,518 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,522 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,577 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,582 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,638 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,643 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,699 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,704 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,760 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,765 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,819 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,823 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,879 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,883 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,941 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:42,945 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:42,999 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,004 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,059 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,063 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,116 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,120 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,175 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,180 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,233 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,238 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,292 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,296 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,349 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,354 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,407 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,411 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,465 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.239.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:55:43,469 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:55:43,528 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.40 INFO 2025-06-26 05:55:43,570 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.40 INFO 2025-06-26 05:55:43,612 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.40 INFO 2025-06-26 05:55:43,655 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 05:55:43,698 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:55:43,741 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_align.nc INFO 2025-06-26 05:55:43,816 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 05:55:43,819 process.py resample():273 [1] Resampling steps for 2004.239.01 INFO 2025-06-26 05:55:43,819 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 05:55:43,845 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_align.nc mission netCDF file INFO 2025-06-26 05:55:43,851 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_align.nc mission netCDF file INFO 2025-06-26 05:55:43,853 resample.py get_mission_start_end():1145 [1] navigation: 2004-08-26T16:27:32.284902144 to 2004-08-26T21:00:11.354229248 (0 days 05:35:56.645770752 before mission_end) WARNING 2025-06-26 05:55:43,854 resample.py get_mission_start_end():1156 [1] Instrument navigation has a gap > 5 minutes at the end of the mission: 0 days 05:35:56.645770752 INFO 2025-06-26 05:55:43,855 resample.py get_mission_start_end():1145 [1] hs2 : 2004-08-26T16:27:13.616181120 to 2004-08-26T21:00:11.344229760 (0 days 05:35:56.655770240 before mission_end) WARNING 2025-06-26 05:55:43,857 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 05:35:56.655770240 INFO 2025-06-26 05:55:43,858 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-08-26T16:27:20.705695360 to 2004-08-26T21:00:11.334230400 (0 days 05:35:56.665769600 before mission_end) WARNING 2025-06-26 05:55:43,859 resample.py get_mission_start_end():1156 [1] Instrument ctd1 has a gap > 5 minutes at the end of the mission: 0 days 05:35:56.665769600 INFO 2025-06-26 05:55:43,861 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-08-26T16:27:20.695696128 to 2004-08-26T21:00:11.304232576 (0 days 05:35:56.695767424 before mission_end) WARNING 2025-06-26 05:55:43,862 resample.py get_mission_start_end():1156 [1] Instrument ctd2 has a gap > 5 minutes at the end of the mission: 0 days 05:35:56.695767424 INFO 2025-06-26 05:55:43,863 resample.py get_mission_start_end():1145 [1] isus : 2004-08-26T13:50:38.000000000 to 2004-08-27T02:36:08.000000000 (0 days 00:00:00 before mission_end) INFO 2025-06-26 05:55:43,865 resample.py get_mission_start_end():1145 [1] biolume : 2004-08-26T16:27:08.786477568 to 2004-08-26T21:00:10.384261376 (0 days 05:35:57.615738624 before mission_end) WARNING 2025-06-26 05:55:43,866 resample.py get_mission_start_end():1156 [1] Instrument biolume has a gap > 5 minutes at the end of the mission: 0 days 05:35:57.615738624 INFO 2025-06-26 05:55:43,868 resample.py get_mission_start_end():1145 [1] tailcone : 2004-08-26T16:27:11.186347520 to 2004-08-26T21:00:11.254236032 (0 days 05:35:56.745763968 before mission_end) WARNING 2025-06-26 05:55:43,869 resample.py get_mission_start_end():1156 [1] Instrument tailcone has a gap > 5 minutes at the end of the mission: 0 days 05:35:56.745763968 INFO 2025-06-26 05:55:43,869 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_align.nc mission netCDF file INFO 2025-06-26 05:55:43,870 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,057 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,058 resample.py resample_variable():1038 [1] Padding navigation_roll with 0 days 05:35:56.645770752 of NaNs to the end of mission INFO 2025-06-26 05:55:44,095 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,095 resample.py resample_variable():1038 [1] Padding navigation_pitch with 0 days 05:35:56.645770752 of NaNs to the end of mission INFO 2025-06-26 05:55:44,132 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,132 resample.py resample_variable():1038 [1] Padding navigation_yaw with 0 days 05:35:56.645770752 of NaNs to the end of mission INFO 2025-06-26 05:55:44,168 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,168 resample.py resample_variable():1038 [1] Padding navigation_mWaterSpeed with 0 days 05:35:56.645770752 of NaNs to the end of mission INFO 2025-06-26 05:55:44,200 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,200 resample.py resample_variable():1038 [1] Padding hs2_bbp470 with 0 days 05:35:56.655770240 of NaNs to the end of mission INFO 2025-06-26 05:55:44,235 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,235 resample.py resample_variable():1038 [1] Padding hs2_bbp676 with 0 days 05:35:56.655770240 of NaNs to the end of mission INFO 2025-06-26 05:55:44,267 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,267 resample.py resample_variable():1038 [1] Padding hs2_fl676 with 0 days 05:35:56.655770240 of NaNs to the end of mission INFO 2025-06-26 05:55:44,298 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,298 resample.py resample_variable():1038 [1] Padding ctd1_temperature with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,328 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,328 resample.py resample_variable():1038 [1] Padding ctd1_conductivity with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,357 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,358 resample.py resample_variable():1038 [1] Padding ctd1_salinity with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,386 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,387 resample.py resample_variable():1038 [1] Padding ctd1_temperature_onboard with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,416 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,416 resample.py resample_variable():1038 [1] Padding ctd1_conductivity_onboard with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,445 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,445 resample.py resample_variable():1038 [1] Padding ctd1_dissolvedO2 with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,474 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,475 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_mll with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,504 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,504 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_umolkg with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,533 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,534 resample.py resample_variable():1038 [1] Padding ctd1_flow1 with 0 days 05:35:56.665769600 of NaNs to the end of mission INFO 2025-06-26 05:55:44,565 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,565 resample.py resample_variable():1038 [1] Padding ctd2_temperature with 0 days 05:35:56.695767424 of NaNs to the end of mission INFO 2025-06-26 05:55:44,597 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,597 resample.py resample_variable():1038 [1] Padding ctd2_conductivity with 0 days 05:35:56.695767424 of NaNs to the end of mission INFO 2025-06-26 05:55:44,627 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,627 resample.py resample_variable():1038 [1] Padding ctd2_salinity with 0 days 05:35:56.695767424 of NaNs to the end of mission INFO 2025-06-26 05:55:44,658 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,658 resample.py resample_variable():1038 [1] Padding ctd2_temperature_onboard with 0 days 05:35:56.695767424 of NaNs to the end of mission INFO 2025-06-26 05:55:44,688 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,689 resample.py resample_variable():1038 [1] Padding ctd2_conductivity_onboard with 0 days 05:35:56.695767424 of NaNs to the end of mission INFO 2025-06-26 05:55:44,720 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,720 resample.py resample_variable():1038 [1] Padding ctd2_flow2 with 0 days 05:35:56.695767424 of NaNs to the end of mission INFO 2025-06-26 05:55:44,740 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,756 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,771 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,786 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,786 resample.py resample_variable():1038 [1] Padding biolume_flow with 0 days 05:35:57.615738624 of NaNs to the end of mission INFO 2025-06-26 05:55:44,822 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 05:55:44,822 resample.py resample_variable():1038 [1] Padding tailcone_propRpm with 0 days 05:35:56.745763968 of NaNs to the end of mission INFO 2025-06-26 05:55:45,011 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_1S.nc INFO 2025-06-26 05:55:46,084 create_products.py gulper_odv():401 [1] No gulper times found for 2004.239.01 INFO 2025-06-26 05:55:46,084 process.py archive():337 [1] Archiving steps for 2004.239.01 INFO 2025-06-26 05:55:46,085 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01, BASE_PATH = /data/auv_data INFO 2025-06-26 05:55:46,086 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 05:55:46,087 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.239.01_1S.nc INFO 2025-06-26 05:55:46,104 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:55:46,105 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.239.01_cal.nc INFO 2025-06-26 05:55:46,174 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:55:46,175 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.239.01_align.nc INFO 2025-06-26 05:55:46,247 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 05:55:46,271 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,293 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,297 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,313 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,354 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,361 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,378 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,397 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,447 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004239/2004.239.01 done. INFO 2025-06-26 05:55:46,448 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 05:55:46,448 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.239.01/dorado_2004.239.01_processing.log /Volumes/AUVCTD/surveys/2004/netcdf