INFO 2025-06-26 12:33:20,687 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 12:33:20,687 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled files exist in archive, but not processed by reprocess_surveys.m INFO 2025-06-26 12:33:20,688 process.py process_mission():449 [1] Processing AUVCTD mission 2007.094.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:33:20,688 process.py download_process():165 [1] Download and processing steps for 2007.094.02 INFO 2025-06-26 12:33:20,688 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007094/2007.094.02 INFO 2025-06-26 12:33:20,688 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007094/2007.094.02 to /data/auv_data/dorado/missionlogs/2007.094.02 INFO 2025-06-26 12:33:25,822 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.094.02 INFO 2025-06-26 12:33:25,822 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/ctdDriver.log (15725731 bytes) INFO 2025-06-26 12:33:26,986 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.094.02/ctdDriver.log: [ 802 979 1389 2562 3551 9258 10469 13865 23838 24754 47264 77255 117929 148274 173113] INFO 2025-06-26 12:33:27,040 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/ctdDriver2.log (15726517 bytes) INFO 2025-06-26 12:33:28,190 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.094.02/ctdDriver2.log: [ 800 977 1387 2559 3548 24751 32256 117937 131958 150239 168206] INFO 2025-06-26 12:33:28,246 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/gps.log (39668 bytes) INFO 2025-06-26 12:33:28,258 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/hydroscatlog.log (10738034 bytes) INFO 2025-06-26 12:33:29,533 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.094.02/hydroscatlog.log: [ 4 33 91 320 544 732 733 849 1055 1110 1618 2181 2196 2249 2273 2683 2828 3469 3487 3506 4916 4939 5201 5324 5799 6028 7318 7427 7744 9411 9687 10499 10625 11393 11457 11458 11938 12049 13164 14118 19746 22288 22289 23880 24123 24933 25787 26080 29730 29883 29927 32899 34030 35809 38109 39729 40012 42057 44785 48983 49876 56595 61350 62147 68463 69623 76733 83448 85993 87497 89800 92469 96873 98795 101369 102171 103589 107671 111574 115528 116590 118255 122473 129193 130448 136204 138405 138877 146700 147855 150480 152478 157088 165733 170727 173370 175148 177441] INFO 2025-06-26 12:33:29,569 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/navigation.log (52716862 bytes) INFO 2025-06-26 12:33:33,391 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/isuslog.log (1021301 bytes) INFO 2025-06-26 12:33:33,496 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/parosci.log (22833206 bytes) INFO 2025-06-26 12:33:35,449 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.094.02/parosci.log: [ 16 17 18 35 36 67 72 147 148 268 269 271 295 298 299 300 332 333 334 662 663 877 878 1126 1127 1128 1497 1498 1854 1855 1856 2300 2301 2302 2438 2773 2774 2775 2776 2842 2844 2845 2912 3106 3107 3108 3110 4005 4006 4007 4111 4155 4260 4262 4263 4338 4988 5190 5870 5989 5990 5992 6009 6010 6224 6337 6338 7156 7158 7544 8620 8621 8622 8757 8848 8849 9241 9242 9243 9289 9291 9343 9608 9609 9611 9805 10349 10689 12769 13457 13458 13459 13729 13730 13836 13876 14162 14164 14752 15417 15418 15419 15568 15569 15570 17111 17112 17113 19449 19737 19738 19739 20177 20178 20179 20422 20424 20718 23026 23027 23028 23313 23314 23680 23681 25007 25008 25741 25742 28227 28228 28229 29630 29631 29632 30267 30269 30270 30677 30958 30959 30960 31716 34971 37264 37266 37504 38562 38563 41089 41806 41809 43287 43288 43289 44479 44480 44481 45392 45393 45394 45455 45456 49584 49586 52451 52453 53012 53014 53015 56303 56304 56305 59209 59210 59211 61131 62296 62297 62298 63017 63432 63433 66235 67602 67604 67983 67984 68069 68071 68072 68498 68499 68500 68501 69539 77949 77950 78974 78975 79378 79379 79380 79381 84536 84537 84538 86189 86190 86191 87397 87398 90402 90403 90404 94299 94300 94301 96826 101761 101763 101764 106157 106158 106159 106316 106317 106318 107461 107462 107463 107465 108290 111525 111526 111527 114687 114688 114689 117080 117081 117082 117962 118769 118770 118772 119005 119007 126113 130160 130161 141243 141244 141245 142729 142731 142732 149111 149113 149114 163037 165151 165152 165427 168229 175639 175640 176372 178355 178356 178357 178358 181932 181933 181934 185021 185023 185924 186073 186074 187481 187482 190186 199141 199142 203920 203922 204627 204628 204629 205881 206466 206467 214127 214129 219749 219750 219752 221769 225813 238651 238652 238654 242833 242834 244440 245746 257455 257456 257556 257557 257558 259369 259370 259371 262564 262565 262567 268008 268009 271207 271208 271209 271210 271537 271538 271540 271541 276288 286157 286158 286523 286524 286525 289352 295384 295385 305581 309877 325520 325521 328873 328874 330214 330215 330216 331383 333216 343396 345473 351672 352125 352126 352128 355317 355319 364558 364560 364586 364587 365428 365429 367893 369147 371041 373904 373905 373907 373908 382439 382440 382442 385375 389958 389959 393026 393028 400294 400295 400297 408873 408874 415474 415475 417596 417597 418159 418740 418741 425275 425276 427792 427793 436016 438961 438962 438964 440591 445221 445222 445223 446707 450701 457608 457609 458209 458210 458211 460902 460903 465624 465625 471730] INFO 2025-06-26 12:33:35,511 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/tailCone.log (10710187 bytes) INFO 2025-06-26 12:33:36,829 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.094.02/biolume.log (12181660 bytes) INFO 2025-06-26 12:33:37,969 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:33:38,571 logs2netcdfs.py download_process_logs():807 [1] Time to process: 12.75 seconds WARNING 2025-06-26 12:33:38,571 process.py download_process():196 [1] No lopc.bin file for 2007.094.02 INFO 2025-06-26 12:33:38,571 process.py calibrate():227 [1] Calibration steps for 2007.094.02 INFO 2025-06-26 12:33:38,944 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 12:33:38,946 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:33:39,699 calibrate.py _nudge_pos():1806 [1] 104: 0.200 -0.0008531 0.0004185 4975 16.74 -7.565 4.631 2007-04-04T15:54:39.998329344 INFO 2025-06-26 12:33:39,739 calibrate.py _nudge_pos():1806 [1] 108: 0.010 0.0000429 0.0000156 150 0.50 12.839 5.836 2007-04-04T15:55:13.196055296 INFO 2025-06-26 12:33:40,311 calibrate.py _nudge_pos():1806 [1] 163: 0.010 -0.0014788 0.0010989 4280 14.35 -15.301 14.193 2007-04-04T16:10:28.193373440 INFO 2025-06-26 12:33:40,370 calibrate.py _nudge_pos():1806 [1] 169: 0.200 0.0000438 0.0000074 114 0.38 17.267 3.651 2007-04-04T16:10:56.001468672 INFO 2025-06-26 12:33:40,884 calibrate.py _nudge_pos():1806 [1] 222: 0.200 -0.0029985 0.0021876 10670 35.66 -12.477 11.368 2007-04-04T16:47:28.001306368 INFO 2025-06-26 12:33:40,924 calibrate.py _nudge_pos():1806 [1] 226: 0.200 -0.0000781 0.0000412 88 0.29 -39.499 26.057 2007-04-04T16:47:48.999867648 INFO 2025-06-26 12:33:41,440 calibrate.py _nudge_pos():1806 [1] 279: 0.010 -0.0030182 0.0019008 10804 36.08 -12.408 9.762 2007-04-04T17:24:46.197979136 INFO 2025-06-26 12:33:42,001 calibrate.py _nudge_pos():1806 [1] 335: 0.010 -0.0034002 0.0019107 10635 35.48 -14.210 9.979 2007-04-04T18:01:10.198364928 INFO 2025-06-26 12:33:42,468 calibrate.py _nudge_pos():1806 [1] 382: 0.010 0.0024160 0.0008268 9149 30.53 11.734 5.018 2007-04-04T18:32:28.199713280 INFO 2025-06-26 12:33:42,744 calibrate.py _nudge_pos():1806 [1] 410: 0.020 -0.0019041 0.0003647 3820 12.75 -22.148 5.302 2007-04-04T18:45:40.195457792 INFO 2025-06-26 12:33:43,307 calibrate.py _nudge_pos():1806 [1] 467: 0.020 0.0013068 0.0009934 5025 16.76 11.558 10.982 2007-04-04T19:03:22.192705792 INFO 2025-06-26 12:33:43,397 calibrate.py _nudge_pos():1806 [1] 476: 0.010 0.0034133 -0.0011873 21240 70.86 7.141 -3.105 2007-04-04T20:14:22.200875264 INFO 2025-06-26 12:33:44,027 calibrate.py _nudge_pos():1862 [1] 503: - - - 139971 467.02 - - INFO 2025-06-26 12:33:44,027 calibrate.py _nudge_pos():1868 [1] Points in final series = 223281 WARNING 2025-06-26 12:33:51,618 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:34:14,088 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 15974 of 178854 INFO 2025-06-26 12:34:15,458 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: 5 seconds INFO 2025-06-26 12:34:28,095 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 5 seconds INFO 2025-06-26 12:34:29,449 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 5 seconds INFO 2025-06-26 12:34:29,452 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.094.02/ctd1.nc INFO 2025-06-26 12:34:29,454 calibrate.py _range_qc_combined_nc():898 [1] Setting 6 ctd1_salinity values to NaN INFO 2025-06-26 12:34:29,454 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 12:34:29,455 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:34:39,334 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 5 seconds INFO 2025-06-26 12:34:40,669 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 5 seconds INFO 2025-06-26 12:34:40,672 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.094.02/ctd2.nc INFO 2025-06-26 12:34:40,673 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 12:34:40,674 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 12:34:40,674 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:34:40,814 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:34:42,892 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 2663889 2663890 2663891] INFO 2025-06-26 12:34:43,287 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: 4 seconds ERROR 2025-06-26 12:34:43,293 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 12:34:43,294 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.094.02 ERROR 2025-06-26 12:34:43,294 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.094.02 INFO 2025-06-26 12:34:43,466 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_cal.nc INFO 2025-06-26 12:34:57,433 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 12:34:57,437 process.py align():251 [1] Alignment steps for 2007.094.02 INFO 2025-06-26 12:34:57,474 align.py process_cal():139 [1] Processing dorado_2007.094.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.094.02 INFO 2025-06-26 12:34:57,534 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:34:57,541 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:34:57,684 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:34:57,692 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:34:57,834 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:34:57,843 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:34:57,936 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:34:57,936 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:34:57,992 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:34:58,001 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:34:58,139 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:34:58,147 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.64 INFO 2025-06-26 12:34:58,263 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:34:58,270 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.64 INFO 2025-06-26 12:34:58,385 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:34:58,392 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.64 INFO 2025-06-26 12:34:58,509 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:58,517 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:58,644 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:58,651 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:58,772 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:58,779 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:58,902 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:58,911 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,033 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,040 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,164 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,171 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,292 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,301 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,423 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,430 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,550 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,558 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,681 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,687 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,808 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,815 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:34:59,938 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:34:59,946 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:35:00,075 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:35:00,085 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:35:00,206 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:35:00,214 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:35:00,337 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:35:00,344 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:35:00,467 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:35:00,474 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:35:00,596 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.094.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:35:00,603 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:35:00,760 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:35:00,861 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:35:00,963 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:35:01,069 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:35:01,184 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:35:01,278 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_align.nc INFO 2025-06-26 12:35:01,396 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 12:35:01,398 process.py resample():273 [1] Resampling steps for 2007.094.02 INFO 2025-06-26 12:35:01,398 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:35:01,428 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_align.nc mission netCDF file INFO 2025-06-26 12:35:01,435 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_align.nc mission netCDF file INFO 2025-06-26 12:35:01,437 resample.py get_mission_start_end():1145 [1] navigation: 2007-04-04T15:36:48.511731200 to 2007-04-05T04:02:25.397044736 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 12:35:01,439 resample.py get_mission_start_end():1145 [1] hs2 : 2007-04-04T15:36:24.283390976 to 2007-04-05T04:02:25.407043840 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 12:35:01,441 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-04-04T15:36:45.181959424 to 2007-04-05T04:02:25.457040640 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:35:01,444 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-04-04T15:36:45.201957888 to 2007-04-05T04:02:25.357047296 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 12:35:01,445 resample.py get_mission_start_end():1145 [1] isus : 2007-04-04T15:37:31.298799872 to 2007-04-05T04:02:24.847082496 (0 days 00:00:00.609958144 before mission_end) INFO 2025-06-26 12:35:01,447 resample.py get_mission_start_end():1145 [1] biolume : 2007-04-04T15:36:15.453961728 to 2007-04-05T04:02:24.177093888 (0 days 00:00:01.279946752 before mission_end) INFO 2025-06-26 12:35:01,449 resample.py get_mission_start_end():1145 [1] tailcone : 2007-04-04T15:36:16.643914240 to 2007-04-05T04:02:25.377046016 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 12:35:01,450 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_align.nc mission netCDF file INFO 2025-06-26 12:35:01,450 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:01,913 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:01,991 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,067 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,142 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,203 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,263 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,322 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,401 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,461 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,519 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,577 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,637 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,697 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,763 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,821 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,879 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:02,940 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,001 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,061 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,121 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,180 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,240 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,264 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,287 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,307 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,331 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,401 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:35:03,752 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_1S.nc INFO 2025-06-26 12:35:11,221 create_products.py gulper_odv():522 [1] Wrote 4 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.094.02/dorado_2007.094.02_1S_Gulper.txt INFO 2025-06-26 12:35:11,221 process.py archive():337 [1] Archiving steps for 2007.094.02 INFO 2025-06-26 12:35:11,222 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02, BASE_PATH = /data/auv_data INFO 2025-06-26 12:35:11,223 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:35:11,224 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.094.02_1S.nc INFO 2025-06-26 12:35:11,258 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:35:11,259 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.094.02_cal.nc INFO 2025-06-26 12:35:11,438 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:35:11,440 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.094.02_align.nc INFO 2025-06-26 12:35:11,599 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:35:11,643 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:11,687 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:11,692 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:11,722 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:11,857 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:11,865 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:11,929 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:11,966 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:12,084 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007094/2007.094.02 done. INFO 2025-06-26 12:35:12,084 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:35:12,085 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.094.02_1S_Gulper.txt INFO 2025-06-26 12:35:12,090 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.094.02/dorado_2007.094.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 12:35:12,090 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.094.02/dorado_2007.094.02_processing.log /Volumes/AUVCTD/surveys/2007/netcdf