INFO 2025-06-26 12:32:43,702 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 12:32:43,702 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled files exist in archive, but not processed by reprocess_surveys.m INFO 2025-06-26 12:32:43,702 process.py process_mission():449 [1] Processing AUVCTD mission 2007.093.12 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:32:43,702 process.py download_process():165 [1] Download and processing steps for 2007.093.12 INFO 2025-06-26 12:32:43,703 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007093/2007.093.12 INFO 2025-06-26 12:32:43,703 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007093/2007.093.12 to /data/auv_data/dorado/missionlogs/2007.093.12 INFO 2025-06-26 12:32:46,223 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.093.12 INFO 2025-06-26 12:32:46,223 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/ctdDriver.log (3786419 bytes) INFO 2025-06-26 12:32:46,503 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.093.12/ctdDriver.log: [ 723 3352 3512 4768 5462 5696 25345 33769 42131] INFO 2025-06-26 12:32:46,516 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/ctdDriver2.log (3785973 bytes) INFO 2025-06-26 12:32:46,801 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.093.12/ctdDriver2.log: [ 722 2119 7981 11993 12213 22437 28748 33769 39472] INFO 2025-06-26 12:32:46,813 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/gps.log (25124 bytes) INFO 2025-06-26 12:32:46,824 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/hydroscatlog.log (2595974 bytes) INFO 2025-06-26 12:32:47,143 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.093.12/hydroscatlog.log: [ 4 12 99 318 330 331 744 1078 1118 1540 1608 1624 1830 2249 2465 2693 3280 3334 3492 3524 3594 3656 3897 4431 5170 5601 7336 8148 10027 10927 10985 11063 11946 12173 13865 16311 16592 18178 18209 18875 19693 22639 24338 25160 27776 27952 28966 32639 33988 38618 41732 42212] INFO 2025-06-26 12:32:47,151 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/navigation.log (12696218 bytes) INFO 2025-06-26 12:32:48,090 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/isuslog.log (244277 bytes) INFO 2025-06-26 12:32:48,118 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/parosci.log (5521718 bytes) INFO 2025-06-26 12:32:48,582 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.093.12/parosci.log: [ 2 3 5 16 17 18 20 42 60 61 140 240 280 281 282 284 289 306 310 312 326 327 328 865 866 867 892 894 895 1104 1105 1381 1382 1384 1932 1933 1934 1986 1987 1988 2080 2218 2219 2290 2291 2423 2747 2748 2831 2868 2911 2912 2917 2918 2974 2976 3030 3031 3032 3884 4098 4112 4276 4319 4320 4354 4392 4393 4394 4866 4867 4868 5157 5825 5987 5988 5990 5991 6023 6024 6288 6289 6290 6353 6354 6373 6374 6376 6565 7547 7549 8731 8874 8875 9287 9552 9554 9555 9556 9718 9720 9825 9826 9827 10574 10576 11775 11777 11779 13072 13073 13129 13731 13732 13873 14191 14192 14331 14491 14873 15658 15659 15660 17724 17726 17727 19493 19494 19495 19926 19927 19928 19929 20419 20628 20629 20630 21477 21478 21480 21656 23888 23889 26649 26650 29043 29044 29199 29200 29405 29406 29407 30424 30735 31755 32030 32347 32348 33383 36841 36842 40041 43347 43348 43805 43806 43807 44543 44544 44545 45901 48315 48317 48318 48397 48398 49828 50162 50163 51948 51949 51950 52336 60189 61230 61231 62418 62419 63853 64378 64380 64697 64699 64830 66665 66666 66667 66669 66885 66886 72315 72316 72317 72465 73845 73846 73848 74312 74313 75331 75332 77004 77712 77713 79095 79096 90371 92286 95702 96972 96973 102346 102347 102348 102349 102715 102716 108621 108622 110998 110999 112660 114854 114856] INFO 2025-06-26 12:32:48,599 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/tailCone.log (2582299 bytes) INFO 2025-06-26 12:32:48,923 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.093.12/biolume.log (2947804 bytes) INFO 2025-06-26 12:32:49,207 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:32:49,372 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.15 seconds WARNING 2025-06-26 12:32:49,372 process.py download_process():196 [1] No lopc.bin file for 2007.093.12 INFO 2025-06-26 12:32:49,372 process.py calibrate():227 [1] Calibration steps for 2007.093.12 INFO 2025-06-26 12:32:49,501 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 12:32:49,503 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:32:50,151 calibrate.py _nudge_pos():1806 [1] 95: 0.080 0.0006126 0.0011547 5596 18.86 4.821 11.343 2007-04-03T15:45:41.148945408 INFO 2025-06-26 12:32:50,718 calibrate.py _nudge_pos():1806 [1] 156: 0.080 0.0006454 0.0014219 11574 38.70 2.476 6.809 2007-04-03T16:25:23.145767424 INFO 2025-06-26 12:32:51,309 calibrate.py _nudge_pos():1806 [1] 219: 0.090 0.0008095 0.0000270 10829 36.16 3.322 0.139 2007-04-03T17:02:35.142865152 INFO 2025-06-26 12:32:51,779 calibrate.py _nudge_pos():1806 [1] 269: 0.080 0.0002849 0.0005207 6006 20.06 2.108 4.809 2007-04-03T17:23:29.146960128 INFO 2025-06-26 12:32:52,302 calibrate.py _nudge_pos():1806 [1] 325: 0.090 0.0017184 0.0014868 18303 61.08 4.175 4.510 2007-04-03T18:25:29.142122752 INFO 2025-06-26 12:32:52,412 calibrate.py _nudge_pos():1862 [1] 303: - - - 2 0.00 - - INFO 2025-06-26 12:32:52,412 calibrate.py _nudge_pos():1868 [1] Points in final series = 53788 WARNING 2025-06-26 12:32:54,265 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:32:59,716 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 2 of 43199 INFO 2025-06-26 12:33:00,060 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:33:03,195 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:33:03,521 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:33:03,523 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.093.12/ctd1.nc INFO 2025-06-26 12:33:03,525 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:33:03,525 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 12:33:03,525 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:33:05,918 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:33:06,254 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:33:06,256 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.093.12/ctd2.nc INFO 2025-06-26 12:33:06,257 calibrate.py _range_qc_combined_nc():898 [1] Setting 167 ctd2_salinity values to NaN INFO 2025-06-26 12:33:06,258 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 12:33:06,258 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:33:06,278 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:33:06,746 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 634044 634045 634046] INFO 2025-06-26 12:33:06,845 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:33:06,850 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 12:33:06,850 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.093.12 ERROR 2025-06-26 12:33:06,850 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.093.12 INFO 2025-06-26 12:33:06,894 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_cal.nc INFO 2025-06-26 12:33:10,281 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 12:33:10,285 process.py align():251 [1] Alignment steps for 2007.093.12 INFO 2025-06-26 12:33:10,312 align.py process_cal():139 [1] Processing dorado_2007.093.12_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.093.12 INFO 2025-06-26 12:33:10,330 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:33:10,332 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:33:10,374 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:33:10,378 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:33:10,418 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:33:10,421 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:33:10,445 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:33:10,445 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:33:10,461 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:33:10,464 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:33:10,503 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:33:10,506 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:33:10,543 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:33:10,546 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:33:10,582 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:33:10,585 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:33:10,622 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,625 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,662 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,665 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,700 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,703 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,739 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,742 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,777 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,781 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,816 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,819 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,855 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,858 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,893 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,897 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,932 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,936 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:10,972 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:10,975 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,011 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:11,015 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,053 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:11,056 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,092 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:11,096 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,132 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:11,135 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,171 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:11,175 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,212 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:11,215 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,252 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.093.12_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:33:11,255 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:33:11,301 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:33:11,335 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:33:11,368 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:33:11,405 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:33:11,442 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:33:11,472 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_align.nc INFO 2025-06-26 12:33:11,535 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 12:33:11,538 process.py resample():273 [1] Resampling steps for 2007.093.12 INFO 2025-06-26 12:33:11,539 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:33:11,563 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_align.nc mission netCDF file INFO 2025-06-26 12:33:11,568 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_align.nc mission netCDF file INFO 2025-06-26 12:33:11,569 resample.py get_mission_start_end():1145 [1] navigation: 2007-04-03T15:25:49.260595200 to 2007-04-03T18:25:40.571339776 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:33:11,571 resample.py get_mission_start_end():1145 [1] hs2 : 2007-04-03T15:25:22.792408576 to 2007-04-03T18:25:40.381352960 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 12:33:11,572 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-04-03T15:25:45.150876672 to 2007-04-03T18:25:40.411350784 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 12:33:11,573 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-04-03T15:25:45.060882944 to 2007-04-03T18:25:40.571339776 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:33:11,575 resample.py get_mission_start_end():1145 [1] isus : 2007-04-03T15:26:31.117727744 to 2007-04-03T18:25:39.781393920 (0 days 00:00:00.789945856 before mission_end) INFO 2025-06-26 12:33:11,576 resample.py get_mission_start_end():1145 [1] biolume : 2007-04-03T15:25:16.012838656 to 2007-04-03T18:25:40.071339776 (0 days 00:00:00.500000 before mission_end) INFO 2025-06-26 12:33:11,577 resample.py get_mission_start_end():1145 [1] tailcone : 2007-04-03T15:25:17.712756480 to 2007-04-03T18:25:40.481346048 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 12:33:11,578 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_align.nc mission netCDF file INFO 2025-06-26 12:33:11,578 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,710 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,734 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,758 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,782 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,803 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,825 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,846 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,867 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,885 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,904 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,923 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,941 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,960 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,979 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:11,997 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,016 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,038 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,060 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,083 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,103 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,124 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,144 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,157 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,168 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,179 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,191 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,216 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:33:12,370 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_1S.nc INFO 2025-06-26 12:33:20,380 create_products.py gulper_odv():522 [1] Wrote 6 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.093.12/dorado_2007.093.12_1S_Gulper.txt INFO 2025-06-26 12:33:20,381 process.py archive():337 [1] Archiving steps for 2007.093.12 INFO 2025-06-26 12:33:20,381 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12, BASE_PATH = /data/auv_data INFO 2025-06-26 12:33:20,381 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:33:20,382 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.093.12_1S.nc INFO 2025-06-26 12:33:20,396 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:33:20,397 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.093.12_cal.nc INFO 2025-06-26 12:33:20,449 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:33:20,450 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.093.12_align.nc INFO 2025-06-26 12:33:20,498 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:33:20,515 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,531 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,535 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,547 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,586 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,592 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,611 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,626 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,658 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007093/2007.093.12 done. INFO 2025-06-26 12:33:20,658 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:33:20,661 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.093.12_1S_Gulper.txt INFO 2025-06-26 12:33:20,666 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.093.12/dorado_2007.093.12_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 12:33:20,666 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.093.12/dorado_2007.093.12_processing.log /Volumes/AUVCTD/surveys/2007/netcdf