INFO 2025-06-26 13:45:13,820 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 13:45:13,820 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Bellingham internal waves near MISO - ctdToUse = ctd1 INFO 2025-06-26 13:45:13,820 process.py process_mission():449 [1] Processing AUVCTD mission 2007.330.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:45:13,820 process.py download_process():165 [1] Download and processing steps for 2007.330.05 INFO 2025-06-26 13:45:13,820 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007330/2007.330.05 INFO 2025-06-26 13:45:13,820 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007330/2007.330.05 to /data/auv_data/dorado/missionlogs/2007.330.05 INFO 2025-06-26 13:45:20,509 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.330.05 INFO 2025-06-26 13:45:20,510 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/ctdDriver.log (19377028 bytes) INFO 2025-06-26 13:45:21,959 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.330.05/ctdDriver.log: [ 195 229 382 392 463 556 729 966 1019 1074 1442 1524 1535 1661 1740 1820 1910 2334 2394 3338 3548 3861 4830 5093 5205 5343 5527 5860 7202 7627 8127 8363 8884 9507 10644 10792 10928 12257 13529 16407 16879 17127 18238 20399 20400 21674 22888 23639 25315 27490 27558 28540 32631 34597 36815 37470 38473 41106 42017 42111 42885 43042 49072 50372 50558 57405 59813 60350 61723 62229 62514 63186 63418 66927 69507 69815 69901 70408 74043 89069 90419 94635 96707 98238 102497 103479 104547 109474 109611 109641 116907 117141 124641 129212 130339 133300 135361 136545 137502 140570 140721 140722 143774 150835 160830 164148 169651 170160 170632 170922 177478 180748 180976 184062 187863 190778 196879 196917 199656 201229 202088 204752 210924 214559 214661 214666 216807] INFO 2025-06-26 13:45:22,054 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/ctdDriver2.log (19376493 bytes) INFO 2025-06-26 13:45:23,533 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.330.05/ctdDriver2.log: [ 229 392 463 556 633 729 968 1021 1525 1661 1740 1820 1909 2334 2396 2898 3553 3866 4836 5099 5211 5349 5533 5866 7209 7507 7632 8133 8835 8890 9513 10650 10798 10933 11435 12263 12512 16412 17131 18242 18482 19582 21678 22891 23642 27493 27561 28543 32633 34599 36817 37471 41105 42015 42109 43039 47809 49069 50367 50554 57401 60346 61719 62224 62510 63181 63413 66921 69809 69895 70403 87123 89062 90413 96701 98233 102492 103474 104542 109604 109634 116901 124635 129206 130333 135354 136538 140564 140715 143767 150828 160822 164040 164142 169645 170154 170626 170916 173629 177476 180745 180972 184058 185170 187860 190775 196876 196916 201227 202085 204749 208995 210922 211217 214555 214656 214661 216802] INFO 2025-06-26 13:45:23,631 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/gps.log (231620 bytes) INFO 2025-06-26 13:45:23,664 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/hydroscatlog.log (13229654 bytes) INFO 2025-06-26 13:45:25,272 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.330.05/hydroscatlog.log: [ 3 5 6 29 42 72 88 101 103 106 238 283 318 329 474 484 533 556 651 728 748 786 788 831 851 855 895 1074 1102 1129 1130 1184 1300 1370 1556 1606 1640 1652 1679 1773 1780 1781 1860 1941 1949 1950 2032 2279 2280 2285 2362 2406 2461 2475 2522 2612 2666 2821 3026 3332 3355 3358 3359 3476 3545 3691 3788 3859 4005 4264 4266 4961 4979 4980 5157 5248 5361 5501 5687 5688 5725 6023 6434 7368 7436 7475 7668 7725 7796 8203 8298 8509 8536 9004 9059 9683 9684 10820 10970 10975 11151 11612 11628 12085 12183 12244 12445 12695 12696 13720 13853 14559 15072 16365 16378 16601 17074 17323 17560 18434 18435 18954 19178 19619 19779 20602 21877 22949 24444 24656 24834 27289 27708 28158 28340 28341 28753 28754 29686 29820 30563 31571 32846 34811 34812 36537 37033 37688 37689 38186 38689 40606 41325 42004 42013 42014 42112 42240 42335 42406 43110 43268 45813 45814 49298 49299 49842 49984 50784 50785 52930 56698 56699 57634 58291 60043 60580 60581 61199 61955 62033 62746 63013 63014 63421 63654 66252 66253 67164 70053 70140 70647 72368 74282 74475 76858 77576 81398 83572 83573 85733 85881 87371 87459 88513 89313 90083 90293 90664 90665 92723 93845 94519 94520 94882 95774 97014 98488 99444 102392 102750 103732 104801 106914 109725 109865 109896 110449 113930 116978 117397 117442 119875 120879 123881 123904 124098 124902 129472 130923 131211 132403 133563 135623 136808 137314 137767 138333 139912 140965 140966 140989 141091 142381 144043 147418 150754 150811 151104 151968 152566 154919 156278 157307 159680 161102 162427 164190 164321 164424 164425 166442 166798 166799 170436 170909 171200 173913 175933 177235 177432 177628 177629 177760 181028 181238 181258 184221 184345 184938 185457 185458 185869 188147 191060 191061 191229 192440 195258 197165 197204 197269 197270 197781 199376 199945 201518 202377 204496 204674 205087 207449 209289 209496 211512 211513 211595 214850 214851 214953 214959 216612 217938] INFO 2025-06-26 13:45:25,319 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/navigation.log (64899418 bytes) INFO 2025-06-26 13:45:30,097 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/isuslog.log (1372053 bytes) INFO 2025-06-26 13:45:30,227 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.330.05/isuslog.log: [1 2 3 4 5 6 7 8] INFO 2025-06-26 13:45:30,231 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/parosci.log (23173430 bytes) INFO 2025-06-26 13:45:32,212 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/tailCone.log (2699611 bytes) INFO 2025-06-26 13:45:32,551 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.330.05/biolume.log (15007196 bytes) INFO 2025-06-26 13:45:34,087 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:45:34,871 logs2netcdfs.py download_process_logs():807 [1] Time to process: 14.36 seconds WARNING 2025-06-26 13:45:34,872 process.py download_process():196 [1] No lopc.bin file for 2007.330.05 INFO 2025-06-26 13:45:34,872 process.py calibrate():227 [1] Calibration steps for 2007.330.05 INFO 2025-06-26 13:45:35,298 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 13:45:35,300 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:45:36,295 calibrate.py _nudge_pos():1806 [1] 122: 0.130 0.0002259 0.0002610 15980 53.81 0.624 0.899 2007-11-27T00:16:35.460989440 INFO 2025-06-26 13:45:36,969 calibrate.py _nudge_pos():1806 [1] 186: 0.140 0.0040606 0.0032635 17850 59.65 10.122 10.139 2007-11-27T01:17:17.461495040 INFO 2025-06-26 13:45:37,650 calibrate.py _nudge_pos():1806 [1] 251: 0.130 0.0004575 0.0002692 14742 49.23 1.381 1.013 2007-11-27T02:07:35.464748032 INFO 2025-06-26 13:45:38,252 calibrate.py _nudge_pos():1806 [1] 308: 0.150 0.0039082 0.0033523 17593 58.76 9.888 10.571 2007-11-27T03:07:17.459364352 INFO 2025-06-26 13:45:38,738 calibrate.py _nudge_pos():1806 [1] 354: 0.150 0.0004842 0.0003013 14334 47.85 1.504 1.167 2007-11-27T03:55:53.459604736 INFO 2025-06-26 13:45:39,348 calibrate.py _nudge_pos():1806 [1] 411: 0.150 0.0039827 0.0033095 17151 57.26 10.341 10.709 2007-11-27T04:54:05.460386304 INFO 2025-06-26 13:45:39,999 calibrate.py _nudge_pos():1806 [1] 472: 0.150 0.0005245 0.0002608 14616 48.80 1.598 0.990 2007-11-27T05:43:53.465693952 INFO 2025-06-26 13:45:40,624 calibrate.py _nudge_pos():1806 [1] 529: 0.150 0.0039147 0.0032938 17209 57.46 10.129 10.621 2007-11-27T06:42:17.465653504 INFO 2025-06-26 13:45:41,305 calibrate.py _nudge_pos():1806 [1] 592: 0.150 0.0005127 0.0003770 15268 50.96 1.495 1.371 2007-11-27T07:34:17.461918976 INFO 2025-06-26 13:45:41,935 calibrate.py _nudge_pos():1806 [1] 649: 0.160 0.0036762 0.0032814 16437 54.86 9.963 11.083 2007-11-27T08:30:05.462565376 INFO 2025-06-26 13:45:42,558 calibrate.py _nudge_pos():1806 [1] 706: 0.170 0.0006334 0.0003021 14929 49.86 1.888 1.123 2007-11-27T09:20:53.463762944 INFO 2025-06-26 13:45:43,638 calibrate.py _nudge_pos():1806 [1] 804: 0.170 0.0039194 0.0033665 16561 55.28 10.542 11.285 2007-11-27T10:17:47.459888128 INFO 2025-06-26 13:45:44,374 calibrate.py _nudge_pos():1806 [1] 870: 0.170 0.0006746 0.0004687 15523 51.81 1.935 1.676 2007-11-27T11:10:41.462454016 INFO 2025-06-26 13:45:45,009 calibrate.py _nudge_pos():1806 [1] 928: 0.180 0.0041012 0.0035093 17298 57.75 10.560 11.261 2007-11-27T12:09:23.461180672 INFO 2025-06-26 13:45:45,783 calibrate.py _nudge_pos():1806 [1] 998: 0.180 0.0006143 0.0003709 14998 50.05 1.824 1.373 2007-11-27T13:00:35.460734464 INFO 2025-06-26 13:45:46,657 calibrate.py _nudge_pos():1806 [1] 1077: 0.180 0.0042692 0.0035403 16528 55.20 11.500 11.885 2007-11-27T13:57:05.458503424 INFO 2025-06-26 13:45:47,266 calibrate.py _nudge_pos():1806 [1] 1133: 0.180 0.0000638 0.0000157 2240 7.48 1.269 0.390 2007-11-27T14:05:29.463976960 INFO 2025-06-26 13:46:10,445 calibrate.py _nudge_pos():1862 [1] 3171: - - - 1 0.00 - - INFO 2025-06-26 13:46:10,445 calibrate.py _nudge_pos():1868 [1] Points in final series = 274976 WARNING 2025-06-26 13:46:10,811 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 13:46:40,638 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:46:56,244 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:46:57,868 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:46:57,872 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.330.05/ctd1.nc INFO 2025-06-26 13:46:57,874 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 13:46:57,875 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 13:46:57,875 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:47:10,231 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:47:11,846 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:47:11,850 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.330.05/ctd2.nc INFO 2025-06-26 13:47:11,851 calibrate.py _range_qc_combined_nc():898 [1] Setting 3 ctd2_salinity values to NaN INFO 2025-06-26 13:47:11,852 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 13:47:11,852 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:47:13,900 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:47:16,550 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3259114 3259115 3259116] INFO 2025-06-26 13:47:17,046 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:47:17,053 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 13:47:17,053 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.330.05 ERROR 2025-06-26 13:47:17,053 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.330.05 INFO 2025-06-26 13:47:17,099 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_cal.nc INFO 2025-06-26 13:47:33,927 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 13:47:33,932 process.py align():251 [1] Alignment steps for 2007.330.05 INFO 2025-06-26 13:47:33,970 align.py process_cal():139 [1] Processing dorado_2007.330.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.330.05 INFO 2025-06-26 13:47:34,042 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:47:34,050 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:47:34,228 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:47:34,238 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:47:34,409 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:47:34,418 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:47:34,523 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:47:34,523 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:47:34,589 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:47:34,599 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:47:34,764 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:34,773 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:34,918 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:34,926 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:35,076 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:35,084 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:35,231 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:35,239 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:35,390 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:35,399 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:35,547 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:35,555 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:35,705 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:35,713 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:35,862 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:35,871 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:36,025 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:36,033 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:36,182 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:36,190 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:36,343 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:36,352 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:36,499 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:36,507 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:36,658 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:36,666 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:36,816 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:36,825 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:36,978 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:36,987 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:37,139 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:37,150 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:37,299 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:37,308 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:37,457 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:37,466 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:37,616 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:37,625 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:37,774 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.330.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:47:37,782 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:47:37,965 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:47:38,086 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:47:38,210 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:47:38,330 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:47:38,459 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 13:47:38,498 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_align.nc INFO 2025-06-26 13:47:38,641 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 13:47:38,643 process.py resample():273 [1] Resampling steps for 2007.330.05 INFO 2025-06-26 13:47:38,644 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:47:38,675 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_align.nc mission netCDF file INFO 2025-06-26 13:47:38,682 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_align.nc mission netCDF file INFO 2025-06-26 13:47:38,684 resample.py get_mission_start_end():1145 [1] navigation: 2007-11-26T23:21:20.598073088 to 2007-11-27T14:40:00.662089984 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:47:38,686 resample.py get_mission_start_end():1145 [1] hs2 : 2007-11-26T23:20:54.749843712 to 2007-11-27T14:40:00.662089984 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:47:38,689 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-11-26T23:21:14.298504704 to 2007-11-27T14:40:00.612093440 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 13:47:38,691 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-11-26T23:21:14.348501248 to 2007-11-27T14:40:00.572096000 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 13:47:38,693 resample.py get_mission_start_end():1145 [1] isus : 2007-11-26T23:21:46.266314752 to 2007-11-27T14:39:59.832146944 (0 days 00:00:00.829943040 before mission_end) INFO 2025-06-26 13:47:38,694 resample.py get_mission_start_end():1145 [1] biolume : 2007-11-26T23:20:44.630502656 to 2007-11-27T14:39:59.892108544 (0 days 00:00:00.769981440 before mission_end) INFO 2025-06-26 13:47:38,696 resample.py get_mission_start_end():1145 [1] tailcone : 2007-11-26T23:20:52.629988864 to 2007-11-27T14:40:00.112127744 (0 days 00:00:00.549962240 before mission_end) INFO 2025-06-26 13:47:38,696 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_align.nc mission netCDF file INFO 2025-06-26 13:47:38,697 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,262 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,353 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,441 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,530 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,605 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,681 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,755 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,828 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,896 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:39,964 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,036 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,105 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,172 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,241 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,309 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,378 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,450 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,522 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,592 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,662 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,733 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,803 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,831 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,858 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,883 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,911 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:40,940 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:47:41,339 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_1S.nc INFO 2025-06-26 13:47:42,985 create_products.py gulper_odv():401 [1] No gulper times found for 2007.330.05 INFO 2025-06-26 13:47:42,986 process.py archive():337 [1] Archiving steps for 2007.330.05 INFO 2025-06-26 13:47:42,986 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05, BASE_PATH = /data/auv_data INFO 2025-06-26 13:47:42,988 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:47:42,989 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.330.05_1S.nc INFO 2025-06-26 13:47:43,035 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:47:43,036 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.330.05_cal.nc INFO 2025-06-26 13:47:43,232 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:47:43,233 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.330.05_align.nc INFO 2025-06-26 13:47:43,416 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:47:43,472 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,527 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,532 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,568 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,729 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,737 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,803 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,817 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,958 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007330/2007.330.05 done. INFO 2025-06-26 13:47:43,958 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:47:43,958 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.330.05/dorado_2007.330.05_processing.log /Volumes/AUVCTD/surveys/2007/netcdf