INFO 2025-06-26 12:27:32,150 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 12:27:32,150 process.py process_mission():434 [1] dorado_info[mission]["comment"] = LOCO mission - 12 m isobath - after Iridium SBD service turned off Got 'Error in plot_sections (line 852)' when reprocessing attempted on 30 May 2018 - ctdToUse = ctd1 INFO 2025-06-26 12:27:32,151 process.py process_mission():449 [1] Processing LOCO mission 2007.009.06 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:27:32,151 process.py download_process():165 [1] Download and processing steps for 2007.009.06 INFO 2025-06-26 12:27:32,151 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007009/2007.009.06 INFO 2025-06-26 12:27:32,151 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007009/2007.009.06 to /data/auv_data/dorado/missionlogs/2007.009.06 INFO 2025-06-26 12:27:34,495 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.009.06 INFO 2025-06-26 12:27:34,496 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/ctdDriver.log (2891635 bytes) INFO 2025-06-26 12:27:34,822 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.009.06/ctdDriver.log: [ 380 750 813 2095 5249 10088 13771 19005 19488 19542 24005 26126 28918 29263] INFO 2025-06-26 12:27:34,830 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/ctdDriver2.log (2891981 bytes) INFO 2025-06-26 12:27:35,039 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.009.06/ctdDriver2.log: [ 14 381 984 2095 2142 2235 3250 5251 8015 10087 10560 16625 16836 19001 26125] INFO 2025-06-26 12:27:35,048 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/gps.log (28508 bytes) INFO 2025-06-26 12:27:35,060 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/hydroscatlog.log (1978994 bytes) INFO 2025-06-26 12:27:35,292 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.009.06/hydroscatlog.log: [ 35 313 496 526 549 979 1060 1076 1096 1115 1524 1619 1988 2251 2293 2327 2997 3320 3389 4187 4999 5098 5177 5345 7514 7599 7759 8011 8110 10184 11176 12022 12054 15290 16857 18661 19590 22944] INFO 2025-06-26 12:27:35,298 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/navigation.log (9674946 bytes) INFO 2025-06-26 12:27:36,017 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/isuslog.log (184501 bytes) INFO 2025-06-26 12:27:36,040 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/parosci.log (4239350 bytes) INFO 2025-06-26 12:27:36,384 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.009.06/parosci.log: [ 1 2 3 4 16 17 18 19 36 38 39 155 156 157 158 305 306 309 310 326 327 328 333 334 666 667 669 893 894 895 896 1381 1383 1384 1523 1953 1954 2033 2294 2295 2297 2467 2670 2671 2747 2748 2883 2884 2977 3030 3031 3055 3056 4043 4112 4257 4261 4359 5342 5343 5345 5879 6001 6002 6003 6049 6160 6241 6501 6502 7210 7211 7589 8945 9071 9509 9510 9511 11430 11431 13155 13156 13364 13365 13367 13840 14287 14289 14507 14907 16665 16666 16667 18134 18135 18136 19728 19729 19989 20099 20322 20324 20325 20752 20754 20755 23822 27254 29603 29905 29907 29970 29971 29972 30367 30892 30893 30894 31120 31121 32177 32262 32461 32462 32463 40932 43275 44426 44776 44777 44779 45442 45443 46673 46674 46675 49957 49958 52446 52591 56585 61441 61442 63119 63120 63929 66652 67056 67057 67059 68037 68038 69028 69989 69990 69991 70260 72720 74403 76038 88094 88095 88096] INFO 2025-06-26 12:27:36,397 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/tailCone.log (1968859 bytes) INFO 2025-06-26 12:27:36,639 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.009.06/biolume.log (2248492 bytes) INFO 2025-06-26 12:27:36,849 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:27:36,975 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.48 seconds WARNING 2025-06-26 12:27:36,976 process.py download_process():196 [1] No lopc.bin file for 2007.009.06 INFO 2025-06-26 12:27:36,976 process.py calibrate():227 [1] Calibration steps for 2007.009.06 INFO 2025-06-26 12:27:37,086 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 12:27:37,088 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:27:37,981 calibrate.py _nudge_pos():1806 [1] 122: 0.030 -0.0000659 -0.0000550 3494 11.76 -0.830 -0.867 2007-01-09T20:48:47.308207616 INFO 2025-06-26 12:27:38,315 calibrate.py _nudge_pos():1806 [1] 158: 0.040 -0.0000843 -0.0000061 6903 23.11 -0.540 -0.049 2007-01-09T21:12:29.310793728 INFO 2025-06-26 12:27:38,335 calibrate.py _nudge_pos():1806 [1] 160: 0.040 -0.0000314 -0.0000710 70 0.23 -20.240 -57.198 2007-01-09T21:12:44.309766144 INFO 2025-06-26 12:27:38,899 calibrate.py _nudge_pos():1806 [1] 221: 0.040 -0.0002069 -0.0004080 5731 19.15 -1.600 -3.949 2007-01-09T21:32:53.306944256 INFO 2025-06-26 12:27:39,279 calibrate.py _nudge_pos():1806 [1] 261: 0.040 -0.0008025 -0.0007842 6459 21.55 -5.516 -6.744 2007-01-09T21:55:05.305696000 INFO 2025-06-26 12:27:39,661 calibrate.py _nudge_pos():1806 [1] 302: 0.040 -0.0010588 -0.0009285 7144 23.83 -6.581 -7.220 2007-01-09T22:19:35.304994048 INFO 2025-06-26 12:27:39,690 calibrate.py _nudge_pos():1806 [1] 305: 0.040 -0.0000058 -0.0000154 60 0.20 -4.354 -14.492 2007-01-09T22:19:49.304035072 INFO 2025-06-26 12:27:40,118 calibrate.py _nudge_pos():1806 [1] 350: 0.040 -0.0023462 -0.0013043 9359 31.23 -11.131 -7.739 2007-01-09T22:51:47.312642560 INFO 2025-06-26 12:27:40,147 calibrate.py _nudge_pos():1806 [1] 353: 0.040 -0.0000355 -0.0000089 70 0.23 -22.861 -7.145 2007-01-09T22:52:03.311546624 INFO 2025-06-26 12:27:40,436 calibrate.py _nudge_pos():1862 [1] 351: - - - 3 0.01 - - INFO 2025-06-26 12:27:40,436 calibrate.py _nudge_pos():1868 [1] Points in final series = 40986 WARNING 2025-06-26 12:27:41,847 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:27:46,201 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:48,557 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:48,805 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:48,806 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.009.06/ctd1.nc INFO 2025-06-26 12:27:48,808 calibrate.py _range_qc_combined_nc():898 [1] Setting 61 ctd1_salinity values to NaN INFO 2025-06-26 12:27:48,808 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 12:27:48,808 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:27:50,631 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:50,891 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:50,893 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.009.06/ctd2.nc INFO 2025-06-26 12:27:50,894 calibrate.py _range_qc_combined_nc():898 [1] Setting 73 ctd2_salinity values to NaN INFO 2025-06-26 12:27:50,894 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 12:27:50,894 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:27:50,911 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:27:51,266 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 83 84 85 86 87 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 300 301 302 303 304 305 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 600 601 602 603 604 605 606 607 608 609 1980 1981 1982 1983 1984 1985 1986 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2280 2281 2282 8460 8461 8462 8463 8464 8465 8466 11220 11221 11222 11223 11224 11225 11226 11227 11228 12180 12181 12182 12183 12184 12185 12186 12187 12188 12189 12190 12191 12192 12193 12194 12195 12196 12197 12198 12199 12200 12201 12202 12203 13140 13141 13142 13143 13144 13145 13146 13147 13148 13149 13150 13151 13152 13153 17460 23640 24300 24301 24302 24303 24304 24305 24306 24307 24308 24309 24310 24311 24312 24313 24314 24315 24316 24317 24318 24319 24320 24321 24322 24323 24324 24325 34080 34081 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78243 78244 78245 78246 78247 78248 78249 78250 78251 78252 78253 78254 78255 80460 80760 80761 80762 80763 80764 80765 80766 80767 80768 80769 80770 80771 80772 80773 80774 80775 84240 84241 84242 84243 84244 84245 94080 94081 94082 94083 94084 94085 94086 94087 94088 94089 94090 94091 94092 94093 94094 94095 94096 94097 102300 102301 102302 102303 102304 102305 102306 102307 102308 102309 102310 102311 102312 102313 102314 102315 102316 102317 102318 102319 102320 111240 112680 112681 112682 112683 112684 112685 112686 112687 112688 112689 112690 112691 112692 112693 112694 112695 112696 112697 112698 112699 112700 112701 112702 112703 120780 120781 120782 120783 120784 120785 120786 120787 120788 120789 120790 120791 120792 120793 120794 120795 120796 120797 120798 120799 120800 120801 120802 120803 122280 122281 122282 122283 122284 122285 122286 122287 122288 122289 122290 122291 122292 157080 157081 157082 157083 157084 157085 157086 157087 157088 160500 160501 160502 160503 160504 160505 160506 160507 166560 166561 166562 166563 166564 166565 166566 166567 166568 166569 166570 166571 166572 166573 166574 166575 166576 166577 166578 166579 166580 166581 166582 166583 166584 166585 168660 168661 173820 173821 173822 175080 175081 175082 175083 175084 175085 175086 175087 175088 175089 175090 175091 175092 189240 189241 189242 189243 189244 189245 189246 189247 189248 189249 189250 189251 207840 207841 207842 207843 207844 207845 207846 207847 207848 207849 207850 207851 207852 207853 207854 207855 207856 207857 207858 253560 253561 253562 253563 253564 253565 253566 253567 253568 253569 253570 253571 255300 255301 255302 255303 255304 255305 280620 280621 280622 280623 280624 280625 280626 280627 280628 280629 280630 280631 280632 280633 280634 280635 287280 287281 287282 287283 287284 287285 287286 287287 287288 287289 287290 287291 287292 287293 287294 287295 288780 288781 288782 288783 288784 288785 288786 288787 288788 288789 288790 288791 288792 288793 288794 288795 288796 288797 288798 288799 288800 288801 288802 288803 288804 288805 288806 288807 288808 295380 295381 295382 295383 354300 354301 354302 354303 354304 354305 354306 354307 354308 354309 354310 361140 361141 361142 381840 381841 381842 381843 381844 381845 381846 381847 381848 381849 381850 381851 381852 381853 381854 381855 408060 408061 408062 408063 408064 408065 408066 408067 408068 408069 408070 408071 408072 408073 408074 417480 417481 417482 417483 417484 417485 417486 417487 417488 417489 417490 417491 417492 417493 417494 417495 479640 479641 479642 479643 479644 479645 479646 479647 494160 494161 494162] INFO 2025-06-26 12:27:51,343 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:27:51,348 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 12:27:51,348 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.009.06 ERROR 2025-06-26 12:27:51,349 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.009.06 INFO 2025-06-26 12:27:51,383 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_cal.nc INFO 2025-06-26 12:27:53,966 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 12:27:53,970 process.py align():251 [1] Alignment steps for 2007.009.06 INFO 2025-06-26 12:27:53,996 align.py process_cal():139 [1] Processing dorado_2007.009.06_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.009.06 INFO 2025-06-26 12:27:54,012 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:54,015 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:54,049 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:54,052 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:54,084 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:54,087 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:54,106 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:27:54,106 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:27:54,120 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:54,123 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:54,156 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:27:54,158 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,189 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:27:54,192 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,221 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:27:54,223 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,253 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,255 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,284 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,287 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,316 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,319 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,349 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,352 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,381 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,384 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,414 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,416 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,446 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,449 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,479 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,482 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,511 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,514 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,544 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,546 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,576 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,579 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,609 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,612 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,642 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,645 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,675 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,678 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,708 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,711 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,741 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,744 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,774 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.009.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:54,776 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:54,814 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:27:54,842 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:27:54,870 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:27:54,900 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:27:54,931 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:27:54,956 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_align.nc INFO 2025-06-26 12:27:55,015 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 12:27:55,018 process.py resample():273 [1] Resampling steps for 2007.009.06 INFO 2025-06-26 12:27:55,018 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:27:55,042 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_align.nc mission netCDF file INFO 2025-06-26 12:27:55,048 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_align.nc mission netCDF file INFO 2025-06-26 12:27:55,050 resample.py get_mission_start_end():1145 [1] navigation: 2007-01-09T20:35:33.522585600 to 2007-01-09T22:52:33.919449856 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 12:27:55,051 resample.py get_mission_start_end():1145 [1] hs2 : 2007-01-09T20:35:08.394306816 to 2007-01-09T22:52:33.929448960 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 12:27:55,052 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-01-09T20:35:30.332803840 to 2007-01-09T22:52:33.929448960 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 12:27:55,054 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-01-09T20:35:30.002826752 to 2007-01-09T22:52:34.059440128 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:27:55,055 resample.py get_mission_start_end():1145 [1] isus : 2007-01-09T20:36:17.089601024 to 2007-01-09T22:52:33.449481984 (0 days 00:00:00.609958144 before mission_end) INFO 2025-06-26 12:27:55,056 resample.py get_mission_start_end():1145 [1] biolume : 2007-01-09T20:34:59.974849536 to 2007-01-09T22:52:33.449447680 (0 days 00:00:00.609992448 before mission_end) INFO 2025-06-26 12:27:55,058 resample.py get_mission_start_end():1145 [1] tailcone : 2007-01-09T20:35:02.264726784 to 2007-01-09T22:52:33.989444864 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 12:27:55,059 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_align.nc mission netCDF file INFO 2025-06-26 12:27:55,060 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,175 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,195 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,215 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,235 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,255 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,273 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,291 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,308 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,324 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,340 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,356 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,373 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,390 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,408 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,424 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,441 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,459 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,475 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,492 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,509 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,526 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,544 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,555 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,565 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,575 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,587 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,607 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:55,747 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_1S.nc INFO 2025-06-26 12:27:57,784 create_products.py gulper_odv():401 [1] No gulper times found for 2007.009.06 INFO 2025-06-26 12:27:57,784 process.py archive():337 [1] Archiving steps for 2007.009.06 INFO 2025-06-26 12:27:57,784 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06, BASE_PATH = /data/auv_data INFO 2025-06-26 12:27:57,785 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:27:57,789 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.009.06_1S.nc INFO 2025-06-26 12:27:57,804 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:27:57,805 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.009.06_cal.nc INFO 2025-06-26 12:27:57,843 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:27:57,844 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.009.06_align.nc INFO 2025-06-26 12:27:57,881 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:27:57,895 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:57,909 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:57,913 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:57,924 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:57,954 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:57,960 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:57,975 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:57,988 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:58,013 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007009/2007.009.06 done. INFO 2025-06-26 12:27:58,014 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:27:58,014 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.009.06/dorado_2007.009.06_processing.log /Volumes/AUVCTD/surveys/2007/netcdf