INFO 2025-06-26 12:19:06,482 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 12:19:06,482 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled files exist in archive, but not processed by reprocess_surveys.m - ctdToUse = ctd1 INFO 2025-06-26 12:19:06,482 process.py process_mission():449 [1] Processing AUVCTD mission 2006.338.11 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:19:06,482 process.py download_process():165 [1] Download and processing steps for 2006.338.11 INFO 2025-06-26 12:19:06,482 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006338/2006.338.11 INFO 2025-06-26 12:19:06,482 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006338/2006.338.11 to /data/auv_data/dorado/missionlogs/2006.338.11 INFO 2025-06-26 12:19:12,286 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.338.11 INFO 2025-06-26 12:19:12,286 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/ctdDriver.log (747 bytes) INFO 2025-06-26 12:19:12,293 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/ctdDriver2.log (741 bytes) INFO 2025-06-26 12:19:12,299 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/gps.log (46940 bytes) INFO 2025-06-26 12:19:12,312 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/hydroscatlog.log (2895374 bytes) INFO 2025-06-26 12:19:12,660 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.338.11/hydroscatlog.log: [ 1 3 4 80 88 93 296 307 572 758 1001 1148 2235 3280 3297 3494 4571 7441 7860 16592 18290 18291 20770 21561 21563 24428 27303 27590 31477 31602 34221 34347 37330 37333 37335 37337 37382 38733 38980 39810 39844 40956 41051 43627 45831 46568 47695] INFO 2025-06-26 12:19:12,666 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/navigation.log (14156822 bytes) INFO 2025-06-26 12:19:13,659 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/isuslog.log (288853 bytes) INFO 2025-06-26 12:19:13,692 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/parosci.log (6194102 bytes) INFO 2025-06-26 12:19:14,207 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.338.11/parosci.log: [ 16 17 19 20 29 30 31 58 59 60 80 81 85 86 160 296 311 312 316 317 318 338 339 871 872 874 900 901 1275 1381 1383 1384 1445 1503 1505 1605 2747 2748 2855 2857 2858 3000 3001 3133 3134 4112 4119 4120 4338 4340 4349 4350 4352 4353 4869 5845 5846 5848 5899 6023 6024 6160 6244 6245 6247 6351 6758 6760 6761 8159 8160 8161 8875 9338 9339 9340 9371 9373 9656 12250 12252 12253 13056 13099 13152 13153 13155 13264 13266 13267 13908 13910 13911 13919 13921 13922 14021 14022 14023 14175 14177 14604 14606 14607 19574 19575 19733 19734 19750 19927 19928 20712 20713 20717 20718 20720 21649 22065 22066 22229 24464 27849 27850 29256 29257 29610 29611 30215 30216 30322 30323 31159 31160 31593 32721 32722 33403 36869 37584 43896 46155 46156 47332 47333 52267 52269 52270 54117 54119 54120 54121 57680 57681 57682 57684 57685 59412 61059 61060 61062 63931 63932 63933 64059 64061 65339 65340 66567 66568 66570 70697 70976 70977 70979 73550 73552 74247 74248 80131 84529 91536 91537 91539 91540 91541 91670 91671 91877 99878 99879 99880 100811 100812 100814 103338 103339 103617 103618 103620 104278 106501 106503 109521 109818 109819 111611 111612 111614 111615 111617 111618 114330 114618 114620 116710 116711 118652 118653 118654 118656 118657 120784 120785 120787 120788 120789 120791 120792 122431 124466 128773] INFO 2025-06-26 12:19:14,227 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/tailCone.log (2714971 bytes) INFO 2025-06-26 12:19:14,583 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.338.11/biolume.log (852901836 bytes) INFO 2025-06-26 12:20:35,073 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:21:16,443 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.338.11/biolume.log: [ 3 6 7 ... 3135650 3135652 3135654] INFO 2025-06-26 12:21:18,944 logs2netcdfs.py download_process_logs():807 [1] Time to process: 126.66 seconds WARNING 2025-06-26 12:21:18,944 process.py download_process():196 [1] No lopc.bin file for 2006.338.11 INFO 2025-06-26 12:21:18,945 process.py calibrate():227 [1] Calibration steps for 2006.338.11 INFO 2025-06-26 12:21:23,411 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 12:21:23,413 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:21:25,103 calibrate.py _nudge_pos():1806 [1] 207: 0.130 -0.0000998 0.0002744 1855 6.25 -2.377 8.140 2006-12-04T17:45:59.194918912 INFO 2025-06-26 12:21:25,691 calibrate.py _nudge_pos():1806 [1] 270: 0.080 -0.0008596 -0.0007713 2970 9.96 -12.829 -14.346 2006-12-04T17:56:59.199705344 INFO 2025-06-26 12:21:26,375 calibrate.py _nudge_pos():1806 [1] 343: 0.150 -0.0010610 -0.0006096 2544 8.50 -18.567 -13.295 2006-12-04T18:06:41.199835648 INFO 2025-06-26 12:21:26,422 calibrate.py _nudge_pos():1806 [1] 348: 0.100 -0.0000353 -0.0000010 59 0.20 -26.660 -0.938 2006-12-04T18:06:57.198739456 INFO 2025-06-26 12:21:26,929 calibrate.py _nudge_pos():1806 [1] 402: 0.120 -0.0029658 -0.0023522 9942 33.25 -13.260 -13.110 2006-12-04T18:41:05.198441984 INFO 2025-06-26 12:21:27,427 calibrate.py _nudge_pos():1806 [1] 454: 0.130 -0.0033401 -0.0022873 10216 34.15 -14.535 -12.412 2006-12-04T19:16:05.194582528 INFO 2025-06-26 12:21:27,946 calibrate.py _nudge_pos():1806 [1] 509: 0.120 -0.0033626 -0.0022373 10240 34.20 -14.607 -12.123 2006-12-04T19:51:11.200311296 INFO 2025-06-26 12:21:28,475 calibrate.py _nudge_pos():1806 [1] 564: 0.120 -0.0024127 0.0003063 10098 33.80 -10.602 1.680 2006-12-04T20:25:53.197684480 INFO 2025-06-26 12:21:29,069 calibrate.py _nudge_pos():1806 [1] 626: 0.160 -0.0016416 -0.0002189 9110 30.48 -7.996 -1.331 2006-12-04T20:57:23.198210816 INFO 2025-06-26 12:21:29,199 calibrate.py _nudge_pos():1862 [1] 606: - - - 3 0.01 - - INFO 2025-06-26 12:21:29,199 calibrate.py _nudge_pos():1868 [1] Points in final series = 59971 WARNING 2025-06-26 12:21:31,281 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:21:37,677 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:21:37,737 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 35 seconds, d_end_time_diff: -12041 seconds INFO 2025-06-26 12:21:37,756 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 35 seconds, d_end_time_diff: -12041 seconds INFO 2025-06-26 12:21:37,757 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.338.11/ctd1.nc INFO 2025-06-26 12:21:37,758 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:21:37,758 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 12:21:37,758 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:21:37,797 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -12041 seconds INFO 2025-06-26 12:21:37,816 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -12041 seconds INFO 2025-06-26 12:21:37,817 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.338.11/ctd2.nc INFO 2025-06-26 12:21:37,818 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 12:21:37,818 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 12:21:37,819 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:21:40,346 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:24:43,585 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 188139476 188139477 188139478] INFO 2025-06-26 12:24:52,276 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 12:25:09,880 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 12:25:09,881 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.338.11 ERROR 2025-06-26 12:25:09,882 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.338.11 INFO 2025-06-26 12:25:09,929 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_cal.nc INFO 2025-06-26 12:25:10,046 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 12:25:10,055 process.py align():251 [1] Alignment steps for 2006.338.11 INFO 2025-06-26 12:25:10,093 align.py process_cal():139 [1] Processing dorado_2006.338.11_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.338.11 INFO 2025-06-26 12:25:10,112 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:25:10,115 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:25:10,159 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:25:10,163 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:25:10,205 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:25:10,209 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:25:10,235 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:25:10,235 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:25:10,253 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:25:10,256 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:25:10,299 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:25:10,302 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:25:10,341 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:25:10,344 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:25:10,383 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:25:10,386 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:25:10,421 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,424 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,443 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,445 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,463 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,465 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,482 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,484 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,502 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,504 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,524 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,526 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,543 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,545 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,563 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,565 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,582 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,584 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,602 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,603 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,622 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,624 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,643 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,646 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,664 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,667 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,685 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,687 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,705 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,708 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,726 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,728 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,745 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.338.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:25:10,747 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = nan INFO 2025-06-26 12:25:10,778 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:25:10,813 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:25:10,850 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:25:11,023 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 94.52 INFO 2025-06-26 12:25:11,506 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.68 INFO 2025-06-26 12:25:11,541 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_align.nc INFO 2025-06-26 12:25:11,657 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 12:25:11,660 process.py resample():273 [1] Resampling steps for 2006.338.11 INFO 2025-06-26 12:25:11,660 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:25:11,693 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_align.nc mission netCDF file INFO 2025-06-26 12:25:11,701 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_align.nc mission netCDF file INFO 2025-06-26 12:25:11,702 resample.py get_mission_start_end():1145 [1] navigation: 2006-12-04T17:36:52.422375168 to 2006-12-04T20:57:36.797279232 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 12:25:11,704 resample.py get_mission_start_end():1145 [1] hs2 : 2006-12-04T17:36:29.113971968 to 2006-12-04T20:57:36.807278336 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:25:11,705 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-12-04T17:36:56.642086144 to 2006-12-04T17:36:56.642086144 (0 days 03:20:40.165192192 before mission_end) WARNING 2025-06-26 12:25:11,706 resample.py get_mission_start_end():1156 [1] Instrument ctd1 has a gap > 5 minutes at the end of the mission: 0 days 03:20:40.165192192 INFO 2025-06-26 12:25:11,707 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-12-04T17:36:56.742079232 to 2006-12-04T17:36:56.742079232 (0 days 03:20:40.065199104 before mission_end) WARNING 2025-06-26 12:25:11,707 resample.py get_mission_start_end():1156 [1] Instrument ctd2 has a gap > 5 minutes at the end of the mission: 0 days 03:20:40.065199104 INFO 2025-06-26 12:25:11,709 resample.py get_mission_start_end():1145 [1] isus : 2006-12-04T17:37:28.989870336 to 2006-12-04T20:57:36.527297536 (0 days 00:00:00.279980800 before mission_end) INFO 2025-06-26 12:25:11,713 resample.py get_mission_start_end():1145 [1] biolume : 2006-12-04T17:36:17.694720000 to 2006-12-04T20:57:36.367274240 (0 days 00:00:00.440004096 before mission_end) INFO 2025-06-26 12:25:11,715 resample.py get_mission_start_end():1145 [1] tailcone : 2006-12-04T17:36:21.574488320 to 2006-12-04T20:57:36.697285888 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 12:25:11,716 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_align.nc mission netCDF file INFO 2025-06-26 12:25:11,717 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,761 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,786 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,812 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,839 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,862 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,885 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,907 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,918 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,918 resample.py resample_variable():1038 [1] Padding ctd1_temperature with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,926 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,926 resample.py resample_variable():1038 [1] Padding ctd1_conductivity with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,933 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,934 resample.py resample_variable():1038 [1] Padding ctd1_salinity with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,941 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,941 resample.py resample_variable():1038 [1] Padding ctd1_temperature_onboard with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,949 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,949 resample.py resample_variable():1038 [1] Padding ctd1_conductivity_onboard with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,956 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,956 resample.py resample_variable():1038 [1] Padding ctd1_dissolvedO2 with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,964 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,964 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_mll with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,971 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,971 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_umolkg with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,979 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,979 resample.py resample_variable():1038 [1] Padding ctd1_flow1 with 0 days 03:20:40.165192192 of NaNs to the end of mission INFO 2025-06-26 12:25:11,988 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,988 resample.py resample_variable():1038 [1] Padding ctd2_temperature with 0 days 03:20:40.065199104 of NaNs to the end of mission INFO 2025-06-26 12:25:11,996 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:11,996 resample.py resample_variable():1038 [1] Padding ctd2_conductivity with 0 days 03:20:40.065199104 of NaNs to the end of mission INFO 2025-06-26 12:25:12,005 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,005 resample.py resample_variable():1038 [1] Padding ctd2_salinity with 0 days 03:20:40.065199104 of NaNs to the end of mission INFO 2025-06-26 12:25:12,014 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,014 resample.py resample_variable():1038 [1] Padding ctd2_temperature_onboard with 0 days 03:20:40.065199104 of NaNs to the end of mission INFO 2025-06-26 12:25:12,023 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,023 resample.py resample_variable():1038 [1] Padding ctd2_conductivity_onboard with 0 days 03:20:40.065199104 of NaNs to the end of mission INFO 2025-06-26 12:25:12,032 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,032 resample.py resample_variable():1038 [1] Padding ctd2_flow2 with 0 days 03:20:40.065199104 of NaNs to the end of mission INFO 2025-06-26 12:25:12,044 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,056 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,067 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,383 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,447 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:25:12,541 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_1S.nc INFO 2025-06-26 12:25:14,397 create_products.py gulper_odv():401 [1] No gulper times found for 2006.338.11 INFO 2025-06-26 12:25:14,397 process.py archive():337 [1] Archiving steps for 2006.338.11 INFO 2025-06-26 12:25:14,397 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11, BASE_PATH = /data/auv_data INFO 2025-06-26 12:25:14,399 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 12:25:14,401 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.338.11_1S.nc INFO 2025-06-26 12:25:14,407 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:25:14,407 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.338.11_cal.nc INFO 2025-06-26 12:25:14,525 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:25:14,526 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.338.11_align.nc INFO 2025-06-26 12:25:14,659 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:25:14,666 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:14,670 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:14,674 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:14,687 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:14,728 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:14,734 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:14,754 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:14,769 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:21,603 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006338/2006.338.11 done. INFO 2025-06-26 12:25:21,603 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:25:21,604 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.338.11/dorado_2006.338.11_processing.log /Volumes/AUVCTD/surveys/2006/netcdf