INFO 2025-06-26 06:11:25,935 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 06:11:25,935 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 8/22/05 - ctdToUse = ctd1 INFO 2025-06-26 06:11:25,935 process.py process_mission():449 [1] Processing BIOLUME mission 2004.349.00 by user docker_user on host 671049448ece INFO 2025-06-26 06:11:25,935 process.py download_process():165 [1] Download and processing steps for 2004.349.00 INFO 2025-06-26 06:11:25,935 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004349/2004.349.00 INFO 2025-06-26 06:11:25,935 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004349/2004.349.00 to /data/auv_data/dorado/missionlogs/2004.349.00 INFO 2025-06-26 06:11:32,178 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.349.00 INFO 2025-06-26 06:11:32,178 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/ctdDriver.log (8320707 bytes) INFO 2025-06-26 06:11:32,795 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/ctdDriver2.log (8241325 bytes) INFO 2025-06-26 06:11:33,388 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.349.00/ctdDriver2.log: [8534] INFO 2025-06-26 06:11:33,413 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/gps.log (56300 bytes) INFO 2025-06-26 06:11:33,428 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/hydroscatlog.log (4283354 bytes) INFO 2025-06-26 06:11:33,939 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/navigation.log (18439675 bytes) INFO 2025-06-26 06:11:35,326 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/isuslog.log (489205 bytes) INFO 2025-06-26 06:11:35,376 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.349.00/isuslog.log: [1 2 3 4 5 6 7] INFO 2025-06-26 06:11:35,378 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/parosci.log (5679158 bytes) INFO 2025-06-26 06:11:35,861 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.349.00/tailCone.log (5679499 bytes) INFO 2025-06-26 06:11:36,584 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.41 seconds WARNING 2025-06-26 06:11:36,584 process.py download_process():196 [1] No lopc.bin file for 2004.349.00 INFO 2025-06-26 06:11:36,584 process.py calibrate():227 [1] Calibration steps for 2004.349.00 INFO 2025-06-26 06:11:36,761 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 06:11:36,763 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 06:11:38,317 calibrate.py _nudge_pos():1806 [1] 182: 0.100 -0.0011767 0.0002391 5969 19.90 -8.760 2.227 2004-12-14T16:37:02.841374848 INFO 2025-06-26 06:11:38,836 calibrate.py _nudge_pos():1806 [1] 236: 0.100 -0.0024720 0.0007867 11134 37.11 -9.870 3.928 2004-12-14T17:15:02.835184768 INFO 2025-06-26 06:11:39,441 calibrate.py _nudge_pos():1806 [1] 299: 0.100 -0.0027639 0.0008777 11570 38.56 -10.624 4.217 2004-12-14T17:54:38.842417024 INFO 2025-06-26 06:11:39,957 calibrate.py _nudge_pos():1806 [1] 352: 0.110 -0.0030098 0.0008297 11860 39.53 -11.291 3.889 2004-12-14T18:35:02.836362112 INFO 2025-06-26 06:11:40,604 calibrate.py _nudge_pos():1806 [1] 417: 0.110 -0.0029398 0.0008252 12783 42.61 -10.234 3.588 2004-12-14T19:18:44.836742912 INFO 2025-06-26 06:11:41,089 calibrate.py _nudge_pos():1806 [1] 467: 0.110 -0.0052009 -0.0000881 12563 41.88 -18.430 -0.390 2004-12-14T20:01:26.841233536 INFO 2025-06-26 06:11:41,556 calibrate.py _nudge_pos():1806 [1] 515: 0.110 0.0000015 -0.0000250 15 0.05 4.624 -99.168 2004-12-14T20:02:16.837808384 INFO 2025-06-26 06:11:41,742 calibrate.py _nudge_pos():1806 [1] 534: 0.110 -0.0037138 -0.0003499 12319 41.06 -13.427 -1.579 2004-12-14T20:43:38.837779712 INFO 2025-06-26 06:11:42,788 calibrate.py _nudge_pos():1806 [1] 641: 0.170 0.0017069 -0.0002626 13600 45.33 5.592 -1.074 2004-12-14T21:30:44.834185856 INFO 2025-06-26 06:11:43,351 calibrate.py _nudge_pos():1806 [1] 699: 0.160 0.0014968 -0.0005139 11744 39.15 5.679 -2.433 2004-12-14T22:10:50.839363072 INFO 2025-06-26 06:11:43,889 calibrate.py _nudge_pos():1806 [1] 754: 0.170 0.0005155 0.0002047 10947 36.50 2.099 1.039 2004-12-14T22:48:14.835638784 INFO 2025-06-26 06:11:44,045 calibrate.py _nudge_pos():1862 [1] 748: - - - 5 0.01 - - INFO 2025-06-26 06:11:44,045 calibrate.py _nudge_pos():1868 [1] Points in final series = 118194 WARNING 2025-06-26 06:11:44,139 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 06:11:44,794 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -5807 seconds INFO 2025-06-26 06:11:45,671 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:11:46,377 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:11:46,379 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.349.00/ctd1.nc INFO 2025-06-26 06:11:46,380 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 06:11:46,380 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 06:11:46,381 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 06:11:51,593 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:11:52,287 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:11:52,290 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.349.00/ctd2.nc WARNING 2025-06-26 06:11:52,291 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (648) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 06:11:52,291 calibrate.py _range_qc_combined_nc():898 [1] Setting 648 ctd2_salinity values to NaN INFO 2025-06-26 06:11:52,292 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 06:11:52,292 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 06:11:53,020 calibrate.py process_logs():3542 [1] Error processing biolume: biolume has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.349.00 ERROR 2025-06-26 06:11:53,021 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.349.00 ERROR 2025-06-26 06:11:53,021 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.349.00 INFO 2025-06-26 06:11:53,114 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_cal.nc INFO 2025-06-26 06:11:56,168 calibrate.py write_netcdf():3512 [1] Data variables written: 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 06:11:56,173 process.py align():251 [1] Alignment steps for 2004.349.00 INFO 2025-06-26 06:11:56,200 align.py process_cal():139 [1] Processing dorado_2004.349.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.349.00 INFO 2025-06-26 06:11:56,235 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:11:56,240 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:11:56,338 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:11:56,345 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:11:56,432 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:11:56,438 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:11:56,489 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 06:11:56,489 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 06:11:56,525 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:11:56,531 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:11:56,611 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:11:56,617 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:56,678 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:11:56,683 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:56,743 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:11:56,748 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:56,812 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:56,817 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:56,889 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:56,895 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:56,968 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:56,973 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,046 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,052 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,126 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,132 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,211 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,216 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,291 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,296 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,368 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,373 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,446 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,451 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,526 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,530 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:11:57,611 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,616 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:11:57,696 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,700 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:11:57,772 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,777 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:11:57,851 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,855 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:11:57,927 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:57,932 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:11:58,016 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:58,021 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:11:58,100 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.349.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:11:58,105 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:11:58,188 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:11:58,238 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:11:58,287 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:11:58,338 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:11:58,394 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_align.nc INFO 2025-06-26 06:11:58,474 align.py write_netcdf():342 [1] Data variables written: 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 06:11:58,477 process.py resample():273 [1] Resampling steps for 2004.349.00 INFO 2025-06-26 06:11:58,477 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 06:11:58,502 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_align.nc mission netCDF file INFO 2025-06-26 06:11:58,507 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_align.nc mission netCDF file INFO 2025-06-26 06:11:58,509 resample.py get_mission_start_end():1145 [1] navigation: 2004-12-14T16:14:29.844061568 to 2004-12-14T22:48:30.834542720 (0 days 00:00:00.159989120 before mission_end) INFO 2025-06-26 06:11:58,511 resample.py get_mission_start_end():1145 [1] hs2 : 2004-12-14T16:14:12.835226752 to 2004-12-14T21:11:44.582298240 (0 days 01:36:46.412233600 before mission_end) WARNING 2025-06-26 06:11:58,512 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 01:36:46.412233600 INFO 2025-06-26 06:11:58,513 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-12-14T16:14:34.903715072 to 2004-12-14T22:48:30.854541568 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 06:11:58,515 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-12-14T16:14:27.934192384 to 2004-12-14T22:48:30.904538112 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 06:11:58,516 resample.py get_mission_start_end():1145 [1] isus : 2004-12-14T16:15:08.511412864 to 2004-12-14T22:48:29.464636800 (0 days 00:00:01.529895040 before mission_end) INFO 2025-06-26 06:11:58,518 resample.py get_mission_start_end():1145 [1] tailcone : 2004-12-14T16:14:07.815570560 to 2004-12-14T22:48:30.994531840 (0 days 00:00:00 before mission_end) INFO 2025-06-26 06:11:58,518 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_align.nc mission netCDF file INFO 2025-06-26 06:11:58,519 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,774 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,818 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,860 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,903 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,935 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,935 resample.py resample_variable():1038 [1] Padding hs2_bbp470 with 0 days 01:36:46.412233600 of NaNs to the end of mission INFO 2025-06-26 06:11:58,967 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,967 resample.py resample_variable():1038 [1] Padding hs2_bbp676 with 0 days 01:36:46.412233600 of NaNs to the end of mission INFO 2025-06-26 06:11:58,998 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:58,998 resample.py resample_variable():1038 [1] Padding hs2_fl676 with 0 days 01:36:46.412233600 of NaNs to the end of mission INFO 2025-06-26 06:11:59,036 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,069 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,103 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,137 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,171 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,205 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,239 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,273 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,307 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,344 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,381 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,418 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,455 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,492 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,528 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,546 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,560 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,574 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,614 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 06:11:59,841 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_1S.nc INFO 2025-06-26 06:12:05,383 create_products.py gulper_odv():401 [1] No gulper times found for 2004.349.00 INFO 2025-06-26 06:12:05,383 process.py archive():337 [1] Archiving steps for 2004.349.00 INFO 2025-06-26 06:12:05,383 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00, BASE_PATH = /data/auv_data INFO 2025-06-26 06:12:05,385 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 06:12:05,386 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.349.00_1S.nc INFO 2025-06-26 06:12:05,407 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:12:05,408 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.349.00_cal.nc INFO 2025-06-26 06:12:05,493 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:12:05,494 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.349.00_align.nc INFO 2025-06-26 06:12:05,581 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:12:05,609 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,635 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,639 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,656 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,711 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,717 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,737 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,761 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004349/2004.349.00 done. INFO 2025-06-26 06:12:05,762 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 06:12:05,762 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.349.00/dorado_2004.349.00_processing.log /Volumes/AUVCTD/surveys/2004/netcdf