INFO 2025-06-26 10:34:28,983 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 10:34:28,983 process.py process_mission():434 [1] dorado_info[mission]["comment"] = M1.5 to M1 Hans mentioned goofy data from hydroscat on this - ctdToUse = ctd1 INFO 2025-06-26 10:34:28,983 process.py process_mission():449 [1] Processing AUVCTD mission 2005.118.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:34:28,983 process.py download_process():165 [1] Download and processing steps for 2005.118.05 INFO 2025-06-26 10:34:28,983 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005118/2005.118.05 INFO 2025-06-26 10:34:28,983 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005118/2005.118.05 to /data/auv_data/dorado/missionlogs/2005.118.05 INFO 2025-06-26 10:34:29,603 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.118.05 INFO 2025-06-26 10:34:29,603 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/ctdDriver.log (5785163 bytes) INFO 2025-06-26 10:34:30,025 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/ctdDriver2.log (5786037 bytes) INFO 2025-06-26 10:34:30,453 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/gps.log (41108 bytes) INFO 2025-06-26 10:34:30,466 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/hydroscatlog.log (3123254 bytes) INFO 2025-06-26 10:34:30,827 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.118.05/hydroscatlog.log: [10824 10825 10826 10827 10828] INFO 2025-06-26 10:34:30,835 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/navigation.log (19389178 bytes) INFO 2025-06-26 10:34:32,251 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/isuslog.log (328245 bytes) INFO 2025-06-26 10:34:32,289 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/parosci.log (8462822 bytes) INFO 2025-06-26 10:34:32,975 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.118.05/parosci.log: [ 1381 13840 13841 31120 31121 31123 31124 31125 31126 31127 113680 113682 113683] INFO 2025-06-26 10:34:32,998 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/tailCone.log (3949195 bytes) INFO 2025-06-26 10:34:33,486 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.118.05/biolume.log (4479436 bytes) INFO 2025-06-26 10:34:33,908 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:34:34,138 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.53 seconds WARNING 2025-06-26 10:34:34,139 process.py download_process():196 [1] No lopc.bin file for 2005.118.05 INFO 2025-06-26 10:34:34,139 process.py calibrate():227 [1] Calibration steps for 2005.118.05 INFO 2025-06-26 10:34:34,296 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 10:34:34,298 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:34:35,974 calibrate.py _nudge_pos():1806 [1] 192: 0.180 0.0072343 -0.0006303 12066 40.25 26.695 -2.902 2005-04-28T18:31:47.994937216 INFO 2025-06-26 10:34:36,478 calibrate.py _nudge_pos():1806 [1] 244: 0.190 0.0092247 -0.0032824 11383 37.95 36.101 -16.029 2005-04-28T19:10:35.995458176 INFO 2025-06-26 10:34:36,956 calibrate.py _nudge_pos():1806 [1] 294: 0.190 0.0077554 -0.0043036 11243 37.48 30.726 -21.277 2005-04-28T19:48:53.998034176 INFO 2025-06-26 10:34:37,622 calibrate.py _nudge_pos():1806 [1] 362: 0.180 0.0045990 -0.0033904 12080 40.28 16.952 -15.597 2005-04-28T20:30:17.997868544 INFO 2025-06-26 10:34:38,269 calibrate.py _nudge_pos():1806 [1] 428: 0.180 0.0032649 -0.0026809 13325 44.41 10.913 -11.185 2005-04-28T21:15:48.000850688 INFO 2025-06-26 10:34:38,912 calibrate.py _nudge_pos():1806 [1] 493: 0.050 0.0022935 -0.0028086 11318 37.73 9.023 -13.792 2005-04-28T21:54:36.201357824 INFO 2025-06-26 10:34:39,153 calibrate.py _nudge_pos():1806 [1] 517: 0.040 0.0000072 0.0000075 20 0.06 16.905 21.687 2005-04-28T21:55:03.219506944 INFO 2025-06-26 10:34:39,376 calibrate.py _nudge_pos():1806 [1] 539: 0.010 0.0000487 0.0000971 8070 26.90 0.269 0.669 2005-04-28T22:22:18.197503360 INFO 2025-06-26 10:34:39,574 calibrate.py _nudge_pos():1862 [1] 537: - - - 3 0.01 - - INFO 2025-06-26 10:34:39,574 calibrate.py _nudge_pos():1868 [1] Points in final series = 82107 WARNING 2025-06-26 10:34:42,522 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 10:34:49,489 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 2 seconds, d_end_time_diff: -3437 seconds INFO 2025-06-26 10:34:50,126 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:34:50,623 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:34:50,625 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.118.05/ctd1.nc INFO 2025-06-26 10:34:50,626 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 10:34:50,627 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 10:34:50,627 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:34:51,232 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:34:51,756 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:34:51,758 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.118.05/ctd2.nc INFO 2025-06-26 10:34:51,759 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 10:34:51,759 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 10:34:51,759 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:34:51,786 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:34:52,560 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 55500 55501 55502 55503 55504 55505 55506 55507 55508 55509 55510 55511 55512 55513 55514 55515 55516 55517 55518 55519 55520 55521 55522 55523 55524 55525 55526 55527 55528 55529 55530 55531 55532 55533 55534 55535 55536 55537 55538 55539 55540 55541 55542 55543 55544 55545 55546 55547 322260 322261 322262 322263 322264 322265 322266 322267 322268 322269 322270 322271 322272 322273 322274 322275 322276 322277 322278 322279 322280 322281 322282 322283 322284 322285 322286 322287 973020] INFO 2025-06-26 10:34:52,711 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:34:52,717 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 10:34:52,717 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.118.05 ERROR 2025-06-26 10:34:52,717 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.118.05 INFO 2025-06-26 10:34:52,783 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_cal.nc INFO 2025-06-26 10:34:52,880 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 10:34:52,885 process.py align():251 [1] Alignment steps for 2005.118.05 INFO 2025-06-26 10:34:52,915 align.py process_cal():139 [1] Processing dorado_2005.118.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.118.05 INFO 2025-06-26 10:34:52,941 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:34:52,944 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:34:53,006 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:34:53,010 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:34:53,070 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:34:53,074 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:34:53,109 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:34:53,109 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:34:53,133 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:34:53,138 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:34:53,196 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:34:53,200 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,247 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:34:53,250 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,298 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:34:53,302 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,351 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,355 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,410 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,414 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,468 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,472 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,527 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,531 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,583 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,587 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,642 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,646 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,700 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,704 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,757 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,762 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,822 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,826 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,880 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,883 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,936 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,939 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:53,993 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:53,997 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:54,052 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:54,056 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:54,108 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:54,112 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:54,164 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:54,169 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:54,221 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:54,225 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:54,279 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.118.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:34:54,282 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:34:54,351 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 10:34:54,397 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 10:34:54,445 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 10:34:54,494 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:34:54,547 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:34:54,589 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_align.nc INFO 2025-06-26 10:34:54,661 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 10:34:54,664 process.py resample():273 [1] Resampling steps for 2005.118.05 INFO 2025-06-26 10:34:54,664 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:34:54,689 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_align.nc mission netCDF file INFO 2025-06-26 10:34:54,694 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_align.nc mission netCDF file INFO 2025-06-26 10:34:54,696 resample.py get_mission_start_end():1145 [1] navigation: 2005-04-28T17:48:44.011952128 to 2005-04-28T22:22:37.796160640 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:34:54,697 resample.py get_mission_start_end():1145 [1] hs2 : 2005-04-28T17:48:26.333163264 to 2005-04-28T21:25:21.261579520 (0 days 00:57:16.534581120 before mission_end) WARNING 2025-06-26 10:34:54,698 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 00:57:16.534581120 INFO 2025-06-26 10:34:54,699 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-04-28T17:48:41.202144640 to 2005-04-28T22:22:37.776162176 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 10:34:54,701 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-04-28T17:48:41.312137088 to 2005-04-28T22:22:37.666169600 (0 days 00:00:00.129991040 before mission_end) INFO 2025-06-26 10:34:54,702 resample.py get_mission_start_end():1145 [1] isus : 2005-04-28T17:49:38.308232576 to 2005-04-28T22:22:36.576244352 (0 days 00:00:01.219916288 before mission_end) INFO 2025-06-26 10:34:54,703 resample.py get_mission_start_end():1145 [1] biolume : 2005-04-28T17:48:21.423465216 to 2005-04-28T22:22:36.666204032 (0 days 00:00:01.129956608 before mission_end) INFO 2025-06-26 10:34:54,705 resample.py get_mission_start_end():1145 [1] tailcone : 2005-04-28T17:48:23.023390080 to 2005-04-28T22:22:37.796160640 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:34:54,705 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_align.nc mission netCDF file INFO 2025-06-26 10:34:54,706 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:54,889 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:54,922 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:54,954 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:54,985 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,012 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,012 resample.py resample_variable():1038 [1] Padding hs2_bbp470 with 0 days 00:57:16.534581120 of NaNs to the end of mission INFO 2025-06-26 10:34:55,039 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,039 resample.py resample_variable():1038 [1] Padding hs2_bbp676 with 0 days 00:57:16.534581120 of NaNs to the end of mission INFO 2025-06-26 10:34:55,067 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,067 resample.py resample_variable():1038 [1] Padding hs2_fl676 with 0 days 00:57:16.534581120 of NaNs to the end of mission INFO 2025-06-26 10:34:55,096 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,122 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,148 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,174 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,200 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,225 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,250 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,276 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,302 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,330 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,357 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,384 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,411 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,438 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,466 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,480 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,493 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,505 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,520 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,551 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:34:55,739 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_1S.nc INFO 2025-06-26 10:34:58,067 create_products.py gulper_odv():401 [1] No gulper times found for 2005.118.05 INFO 2025-06-26 10:34:58,068 process.py archive():337 [1] Archiving steps for 2005.118.05 INFO 2025-06-26 10:34:58,068 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05, BASE_PATH = /data/auv_data INFO 2025-06-26 10:34:58,069 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:34:58,070 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.118.05_1S.nc INFO 2025-06-26 10:34:58,087 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:34:58,088 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.118.05_cal.nc INFO 2025-06-26 10:34:58,164 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:34:58,165 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.118.05_align.nc INFO 2025-06-26 10:34:58,237 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:34:58,260 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,281 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,286 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,300 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,354 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,360 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,388 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,408 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,461 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005118/2005.118.05 done. INFO 2025-06-26 10:34:58,461 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:34:58,461 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.118.05/dorado_2005.118.05_processing.log /Volumes/AUVCTD/surveys/2005/netcdf