INFO 2025-06-26 12:30:56,494 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 12:30:56,494 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Test AUVCTD mission - First mission with new blunt nose cone Got 'Error in plot_sections (line 852)' when reprocessing attempted on 30 May 2018 - ctdToUse = ctd1 INFO 2025-06-26 12:30:56,494 process.py process_mission():449 [1] Processing AUVCTD mission 2007.061.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:30:56,494 process.py download_process():165 [1] Download and processing steps for 2007.061.02 INFO 2025-06-26 12:30:56,494 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007061/2007.061.02 INFO 2025-06-26 12:30:56,494 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007061/2007.061.02 to /data/auv_data/dorado/missionlogs/2007.061.02 INFO 2025-06-26 12:30:58,848 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.061.02 INFO 2025-06-26 12:30:58,848 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/ctdDriver.log (2691347 bytes) INFO 2025-06-26 12:30:59,048 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.061.02/ctdDriver.log: [ 21 412 628 820 990 1782 2235 2550 3189 5752 5766 6348 10301 10306 16877 17093 18362 21160 25304 25463 27071 28677] INFO 2025-06-26 12:30:59,059 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/ctdDriver2.log (2691253 bytes) INFO 2025-06-26 12:30:59,284 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.061.02/ctdDriver2.log: [ 627 819 990 1030 1643 3185 4828 5748 10300 11956 18362 25462 28676] INFO 2025-06-26 12:30:59,297 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/gps.log (30596 bytes) INFO 2025-06-26 12:30:59,311 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/hydroscatlog.log (1841234 bytes) INFO 2025-06-26 12:30:59,552 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.061.02/hydroscatlog.log: [ 89 93 331 558 837 839 1015 1065 1124 1160 1465 1524 1543 1580 1735 1736 2188 2236 2290 2323 2384 3280 3324 3345 3438 3516 5108 5140 5303 5849 5863 7609 7725 9409 11063 11356 11551 11580 12058 13865 14571 16293 16363 17366 17510 18463 21886 23446 24027 25401 25739 27916] INFO 2025-06-26 12:30:59,559 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/navigation.log (8996682 bytes) INFO 2025-06-26 12:31:00,307 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/isuslog.log (173045 bytes) INFO 2025-06-26 12:31:00,330 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.061.02/isuslog.log: [1 2 4 5 6 7 8] INFO 2025-06-26 12:31:00,331 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/parosci.log (3956966 bytes) INFO 2025-06-26 12:31:00,705 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.061.02/parosci.log: [ 1 2 4 8 9 16 17 19 36 39 40 41 42 63 64 152 294 295 306 343 344 345 349 350 677 679 908 909 1317 1318 1382 1383 1384 1532 1533 1534 2030 2122 2270 2463 2748 2749 2884 2922 2966 3039 3040 3041 3042 3137 3958 4112 4113 4259 4261 4382 4384 4677 4678 5873 5890 6074 6075 6245 6246 6247 6252 6408 6410 7097 7098 8817 8934 8936 8937 8991 8992 8993 8994 9233 9234 9236 9238 9239 9445 9446 9448 10464 10465 10466 10467 10609 11493 11494 13713 13714 13719 13721 13804 13840 13841 13843 14241 15744 15845 15846 15847 19672 19673 19674 19819 20448 20642 20643 20644 20752 20753 20755 20820 20821 24690 24691 26042 26043 27945 27960 29318 29319 29320 30554 30555 30556 30879 30880 30881 31044 31045 31918 36951 39158 39159 41648 43970 43971 43973 44584 44585 44586 45627 45660 46205 46206 46207 49614 57138 61835 63006 64565 64566 64567 67534 68254 69160 69161 69162 69163 69989 69990 69991 73015 79889 79890] INFO 2025-06-26 12:31:00,726 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/tailCone.log (1831675 bytes) INFO 2025-06-26 12:31:00,977 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.061.02/biolume.log (2091820 bytes) INFO 2025-06-26 12:31:01,202 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:31:01,339 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.49 seconds WARNING 2025-06-26 12:31:01,339 process.py download_process():196 [1] No lopc.bin file for 2007.061.02 INFO 2025-06-26 12:31:01,340 process.py calibrate():227 [1] Calibration steps for 2007.061.02 INFO 2025-06-26 12:31:01,460 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 12:31:01,462 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:31:03,268 calibrate.py _nudge_pos():1806 [1] 200: 0.190 -0.0001374 0.0002582 4724 15.88 -1.285 3.013 2007-03-02T17:48:59.698451712 INFO 2025-06-26 12:31:03,929 calibrate.py _nudge_pos():1806 [1] 259: 0.190 0.0009537 0.0011075 11737 39.23 3.609 5.231 2007-03-02T18:29:11.703217920 INFO 2025-06-26 12:31:04,590 calibrate.py _nudge_pos():1806 [1] 318: 0.200 -0.0006932 0.0014830 12233 40.83 -2.520 6.731 2007-03-02T19:10:59.701408512 INFO 2025-06-26 12:31:05,175 calibrate.py _nudge_pos():1806 [1] 372: 0.200 -0.0005387 0.0008770 7554 25.21 -3.172 6.446 2007-03-02T19:37:05.704130048 INFO 2025-06-26 12:31:05,593 calibrate.py _nudge_pos():1862 [1] 379: - - - 2 0.00 - - INFO 2025-06-26 12:31:05,593 calibrate.py _nudge_pos():1868 [1] Points in final series = 37971 WARNING 2025-06-26 12:31:07,033 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:31:11,352 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:31:13,626 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:31:13,866 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:31:13,869 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.061.02/ctd1.nc INFO 2025-06-26 12:31:13,870 calibrate.py _range_qc_combined_nc():898 [1] Setting 55 ctd1_salinity values to NaN INFO 2025-06-26 12:31:13,870 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 12:31:13,871 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:31:15,677 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:31:15,924 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:31:15,926 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.061.02/ctd2.nc WARNING 2025-06-26 12:31:15,928 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (13590) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 12:31:15,928 calibrate.py _range_qc_combined_nc():898 [1] Setting 13590 ctd2_salinity values to NaN INFO 2025-06-26 12:31:15,929 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 12:31:15,929 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:31:16,203 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:31:16,553 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 180 181 182 240 241 242 300 301 302 303 304 305 306 307 308 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 7980 7981 7982 7983 7984 7985 7986 7987 11220 11221 11222 11223 11224 11225 11226 11227 13020 13021 13022 13023 13024 13025 13026 13027 13028 13029 13030 13031 13032 13033 13034 13035 13036 13037 13038 13039 13040 13041 13042 13043 13044 13045 13046 13047 15720 15721 15722 15723 15724 15725 15726 15727 15728 15729 15730 15731 15732 15733 15734 15735 15736 15737 15738 16680 16681 16682 16683 16684 16685 16686 16687 16688 16689 16690 16691 17280 17281 17282 17283 17284 17285 17286 17287 17288 17289 17290 17291 17292 17293 17294 17295 17296 17297 17298 17299 17300 17301 17302 17303 23640 23641 23642 23643 23644 23645 23646 23647 23648 23649 23650 23651 23652 23653 23654 23655 23656 23657 23658 23659 23660 23661 23662 23663 24180 24181 24182 24183 24184 24185 24186 24187 24188 24189 24190 24191 24192 24900 24901 24902 24903 24904 24905 24906 24907 24908 24909 34380 34381 34382 34383 34384 34385 34386 34387 34388 34389 34390 34391 34860 34861 34862 34863 34864 34865 34866 34867 34868 34869 34870 34871 34872 49740 49741 49742 49743 49744 49745 49746 49747 49748 49749 50700 50701 50702 50703 50704 50705 50706 50707 52080 52081 52082 52083 52084 52085 52086 52087 52088 52089 52090 52091 52092 52093 52094 52095 52096 55320 59760 59761 59762 59763 74400 74401 74402 74403 74404 74405 74406 74407 74408 74409 74410 74411 74412 74413 74414 74415 74416 74417 74418 74419 74420 74421 74422 74423 74424 74425 74426 74427 74428 74580 74581 74582 74583 74584 77160 77161 77162 77163 77164 77165 77166 77167 77168 77169 77170 77171 77172 77173 77174 77175 77640 77641 77642 77643 77644 77645 77646 77647 77648 77649 77650 77651 77652 77653 77654 77655 77656 77657 77658 78660 78661 78662 78663 78664 78665 78666 78667 78668 78669 78670 78671 78672 78673 78674 78675 78676 78677 78678 78679 78680 78681 78682 78683 78684 78685 78686 78687 78688 78689 80100 80101 80102 80103 88500 88501 111180 111181 111182 111183 111184 111185 111186 111187 111188 111189 111190 111191 111192 111193 111194 111195 111196 111197 114720 114721 114722 114723 114724 114725 114726 114727 114728 115800 115801 115802 115803 115804 115805 115806 115807 115808 115809 115810 115811 115812 115813 115814 115815 115816 115817 115818 115819 115820 115821 115822 115823 115824 138420 138421 138422 138423 138424 138425 138426 138427 138428 138429 138430 138431 138432 138433 138434 138435 138436 138437 138438 138439 138440 138441 138442 138443 138444 141720 141721 141722 141723 141724 141725 141726 141727 141728 156600 156601 156602 156603 156604 156605 156606 156607 156608 156609 156610 156611 156612 156613 156614 164280 170940 170941 170942 170943 170944 170945 170946 170947 170948 170949 170950 170951 170952 171120 171121 171122 171123 171124 171125 171126 171127 171128 171129 171130 171131 171132 171133 171134 171135 171136 171137 171138 171139 171140 171141 171142 171143 171144 171145 171146 171147 171900 171901 171902 171903 171904 171905 171906 171907 171908 171909 174300 174301 178740 178741 178742 178743 178744 178745 178746 178747 178748 178749 178750 178751 178752 178753 178754 178755 178756 178757 206820 206821 206822 206823 206824 206825 206826 206827 206828 206829 206830 206831 206832 206833 206834 206835 206836 206837 206838 233100 233101 233102 233103 233104 233105 233106 233107 233108 233109 233110 233111 233112 233113 233114 233115 233116 233117 233118 233119 233120 233121 233122 255300 255301 255302 255303 255304 255305 255306 255307 255308 255309 255310 255311 255312 255313 255314 255315 255316 255480 255481 255482 255483 255484 255485 255486 255487 255488 255489 255490 255491 255492 255493 255494 255495 255496 255497 255498 255499 255500 255501 258540 258541 258542 258543 258544 258545 258546 258547 258548 258549 258550 258551 258552 258553 258554 258555 258556 352380 352381 352382 352383 352384 352385 352386 352387 352388 352389 352390 352391 352392 352393 352394 352395 352396 352397 352398 382080 382081 382082 382083 382084 382085 382086 382087 382088 382089 382090 382091 382092 382093 382094 386820 386821 386822 386823 386824 386825 386826 386827 386828 386829 386830 386831 386832 386833 386834 386835 386836 386837 391440 391441 391442 391443 391444 391445 391446 391447 391448 391449 391450 432360 432361 432362 432363 432364 432365 446640 446641 446642 446643 446644 446645 446646] INFO 2025-06-26 12:31:16,638 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:31:16,646 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 12:31:16,646 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.061.02 ERROR 2025-06-26 12:31:16,646 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.061.02 INFO 2025-06-26 12:31:16,680 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_cal.nc INFO 2025-06-26 12:31:19,328 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 12:31:19,334 process.py align():251 [1] Alignment steps for 2007.061.02 INFO 2025-06-26 12:31:19,366 align.py process_cal():139 [1] Processing dorado_2007.061.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.061.02 INFO 2025-06-26 12:31:19,383 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:31:19,387 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:31:19,425 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:31:19,429 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:31:19,463 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:31:19,467 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:31:19,486 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:31:19,486 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:31:19,499 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:31:19,503 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:31:19,539 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:31:19,542 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,573 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:31:19,577 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,622 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:31:19,626 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,656 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,659 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,692 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,696 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,726 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,730 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,760 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,764 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,794 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,798 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,831 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,835 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,867 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,872 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,911 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,915 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,948 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,953 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:19,984 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:19,988 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,023 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:20,027 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,060 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:20,064 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,101 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:20,105 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,139 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:20,143 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,175 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:20,179 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,211 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:20,215 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,246 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.061.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:31:20,250 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:31:20,291 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:31:20,328 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:31:20,360 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:31:20,393 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:31:20,429 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:31:20,457 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_align.nc INFO 2025-06-26 12:31:20,523 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 12:31:20,526 process.py resample():273 [1] Resampling steps for 2007.061.02 INFO 2025-06-26 12:31:20,527 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:31:20,556 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_align.nc mission netCDF file INFO 2025-06-26 12:31:20,562 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_align.nc mission netCDF file INFO 2025-06-26 12:31:20,564 resample.py get_mission_start_end():1145 [1] navigation: 2007-03-02T17:30:21.615045888 to 2007-03-02T19:37:46.301348864 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 12:31:20,565 resample.py get_mission_start_end():1145 [1] hs2 : 2007-03-02T17:29:54.466905600 to 2007-03-02T19:37:46.211354880 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 12:31:20,567 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-03-02T17:30:15.665453312 to 2007-03-02T19:37:46.251352320 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 12:31:20,569 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-03-02T17:30:15.615456768 to 2007-03-02T19:37:46.181357056 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 12:31:20,570 resample.py get_mission_start_end():1145 [1] isus : 2007-03-02T17:30:49.423140864 to 2007-03-02T19:37:45.711389184 (0 days 00:00:00.659954944 before mission_end) INFO 2025-06-26 12:31:20,572 resample.py get_mission_start_end():1145 [1] biolume : 2007-03-02T17:29:47.497348864 to 2007-03-02T19:37:45.131394560 (0 days 00:00:01.239949568 before mission_end) INFO 2025-06-26 12:31:20,574 resample.py get_mission_start_end():1145 [1] tailcone : 2007-03-02T17:29:49.697232128 to 2007-03-02T19:37:46.371344128 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:31:20,575 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_align.nc mission netCDF file INFO 2025-06-26 12:31:20,575 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,691 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,714 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,738 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,760 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,783 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,803 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,821 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,840 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,859 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,877 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,898 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,921 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,938 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,956 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,976 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:20,994 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,016 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,036 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,082 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,102 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,122 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,140 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,153 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,165 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,176 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,189 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,211 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:31:21,359 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_1S.nc INFO 2025-06-26 12:31:22,314 create_products.py gulper_odv():401 [1] No gulper times found for 2007.061.02 INFO 2025-06-26 12:31:22,314 process.py archive():337 [1] Archiving steps for 2007.061.02 INFO 2025-06-26 12:31:22,314 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02, BASE_PATH = /data/auv_data INFO 2025-06-26 12:31:22,315 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:31:22,316 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.061.02_1S.nc INFO 2025-06-26 12:31:22,331 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:31:22,332 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.061.02_cal.nc INFO 2025-06-26 12:31:22,373 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:31:22,374 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.061.02_align.nc INFO 2025-06-26 12:31:22,410 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:31:22,424 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,439 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,443 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,454 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,484 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,489 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,508 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,520 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,546 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007061/2007.061.02 done. INFO 2025-06-26 12:31:22,546 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:31:22,547 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.061.02/dorado_2007.061.02_processing.log /Volumes/AUVCTD/surveys/2007/netcdf