INFO 2025-06-26 12:37:42,257 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 12:37:42,257 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD missions - Bellingham looking for internal waves in Southern MB - ctdToUse = ctd1 INFO 2025-06-26 12:37:42,257 process.py process_mission():449 [1] Processing AUVCTD mission 2007.134.09 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:37:42,257 process.py download_process():165 [1] Download and processing steps for 2007.134.09 INFO 2025-06-26 12:37:42,257 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007134/2007.134.09 INFO 2025-06-26 12:37:42,257 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007134/2007.134.09 to /data/auv_data/dorado/missionlogs/2007.134.09 INFO 2025-06-26 12:37:48,685 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.134.09 INFO 2025-06-26 12:37:48,685 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/ctdDriver.log (21772651 bytes) INFO 2025-06-26 12:37:50,268 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.09/ctdDriver.log: [ 23 27 188 220 232 240 430 560 654 688 695 751 973 1009 1091 1316 1451 1493 1527 1586 1783 2016 2100 2165 2548 2745 2917 3067 3192 3346 3528 3680 3851 4178 4188 4834 5018 5266 7228 7289 7554 9472 9607 9908 10639 10718 10819 10902 11270 11798 11826 12639 13474 14485 16018 16110 16207 16507 16893 19007 20990 21803 22313 24204 24827 25332 28563 28931 29640 30083 30248 34425 36006 36075 37748 39061 42691 42867 43516 44935 45529 46176 46280 49792 51023 51638 56306 56507 56617 60404 61822 63223 64345 66029 69579 69939 73305 75855 76619 81032 83979 85658 88536 88856 90083 93229 96036 96299 96798 99314 99893 101473 103542 104762 107195 108957 110194 116939 117308 117563 118544 123657 124423 126046 127865 135597 135647 137085 138087 138233 141999 143803 146099 149773 157234 159313 159994 163950 166431 167105 169069 169247 171054 174218 175097 178555 179251 180977 184094 186054 189366 190732 190808 192854 195558 196900 197271 197526 199607 202674 204217 204801 208563 209648 210960 212785 216063 216905 223561 224015 224388 224550 224974 229976 230057 231068 232709 237821 244536] INFO 2025-06-26 12:37:50,336 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/ctdDriver2.log (21772645 bytes) INFO 2025-06-26 12:37:51,862 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.09/ctdDriver2.log: [ 3 21 25 219 230 238 428 536 558 652 686 693 970 1006 1088 1191 1313 1449 1523 1582 1672 2012 2096 2162 2232 2418 2544 2740 3062 3187 3522 3845 4173 4182 4828 5260 7283 9465 9601 9902 10633 10712 10814 10971 11792 11820 12634 13468 16013 16104 16202 16501 16970 19002 20985 21799 24199 24823 25033 25455 28558 28927 29635 30244 34422 36003 36071 37744 37847 38181 39058 42687 42863 43513 44931 45525 46172 49787 51019 51634 56301 56302 56503 56613 56768 60400 63219 67514 69575 69934 73301 76615 83974 85838 88532 88853 93226 96032 96294 96793 99308 99887 101467 103536 104757 107190 108952 109672 110189 116934 117302 117557 118539 123652 124419 127860 130365 135592 135643 137081 138083 138229 141995 143799 146095 148546 149769 157230 159311 159991 163550 163948 166430 167103 171052 174217 175095 176521 178554 179249 181172 184092 186053 189365 190731 190807 192853 195557 196194 197270 199606 202673 203233 204216 204800 208562 209648 210959 212785 216063 216904 223561 224015 224388 224550 224974 229976 230057 231068 231105 232709 237821 244536] INFO 2025-06-26 12:37:51,929 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/gps.log (99068 bytes) INFO 2025-06-26 12:37:51,948 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/hydroscatlog.log (14844614 bytes) INFO 2025-06-26 12:37:53,638 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.09/hydroscatlog.log: [ 89 109 274 318 327 517 836 907 1059 1060 1096 1115 1280 1403 1580 1669 1912 2253 2323 2453 2512 2636 3005 3280 3321 3434 3435 3617 3940 4919 4922 5107 5354 5367 5656 6444 7376 7640 7982 9360 9558 9995 10725 11063 11885 11913 13561 13866 14539 16292 16667 16978 17060 17799 19091 21073 24286 24910 25415 26661 27780 28582 28645 32024 34506 37929 38066 38264 39139 42943 45604 47417 49866 53362 56376 56577 56687 58597 60473 61891 62089 63291 64413 66097 67584 70004 73368 73593 73990 76416 80074 81091 82199 85900 86751 88592 90139 93284 96023 96089 96352 99365 103132 103591 104812 109527 109726 110242 113199 116984 123698 127905 130409 130410 131572 133113 133585 133586 135633 138270 145797 148619 150549 152909 158789 158790 163976 166457 167129 169093 169271 171076 175116 177400 178573 179268 181192 181350 184110 190744 190820 196910 197536 201066 202679 203571 204223 204806 205004 208059 208567 212172 212787 216063 216904 224011 224546 224970 228102 229971 230052 231061 231126 233860 239176 241080] INFO 2025-06-26 12:37:53,678 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/navigation.log (72914922 bytes) INFO 2025-06-26 12:37:58,877 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/isuslog.log (1390677 bytes) INFO 2025-06-26 12:37:59,010 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.09/isuslog.log: [1 2 3 4 5 6 7 8] INFO 2025-06-26 12:37:59,015 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/parosci.log (26038262 bytes) INFO 2025-06-26 12:38:01,229 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/tailCone.log (3007771 bytes) INFO 2025-06-26 12:38:01,616 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.09/biolume.log (16837756 bytes) INFO 2025-06-26 12:38:03,242 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:38:04,081 logs2netcdfs.py download_process_logs():807 [1] Time to process: 15.40 seconds WARNING 2025-06-26 12:38:04,082 process.py download_process():196 [1] No lopc.bin file for 2007.134.09 INFO 2025-06-26 12:38:04,082 process.py calibrate():227 [1] Calibration steps for 2007.134.09 INFO 2025-06-26 12:38:04,485 calibrate.py _navigation_process():1637 [1] Removing points outside of Monterey Bay for 2007.134.09/navigation.nc INFO 2025-06-26 12:38:04,487 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('navigation_latitude', Range(min=36, max=37)), ('navigation_longitude', Range(min=-122.1, max=-121.7))] INFO 2025-06-26 12:38:04,488 calibrate.py _range_qc_combined_nc():916 [1] navigation_time: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,499 calibrate.py _range_qc_combined_nc():916 [1] navigation_roll: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,503 calibrate.py _range_qc_combined_nc():916 [1] navigation_pitch: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,506 calibrate.py _range_qc_combined_nc():916 [1] navigation_yaw: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,511 calibrate.py _range_qc_combined_nc():916 [1] navigation_posx: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,515 calibrate.py _range_qc_combined_nc():916 [1] navigation_posy: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,519 calibrate.py _range_qc_combined_nc():916 [1] navigation_depth: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,523 calibrate.py _range_qc_combined_nc():916 [1] navigation_mWaterSpeed: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,527 calibrate.py _range_qc_combined_nc():916 [1] navigation_latitude: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,531 calibrate.py _range_qc_combined_nc():916 [1] navigation_longitude: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 12:38:04,542 calibrate.py _range_qc_combined_nc():936 [1] Done range checking navigation INFO 2025-06-26 12:38:04,546 calibrate.py _gps_process():2069 [1] Removing points outside of Monterey Bay for 2007.134.09/gps.nc INFO 2025-06-26 12:38:04,547 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('gps_latitude', Range(min=36, max=37)), ('gps_longitude', Range(min=-122.1, max=-121.7))] INFO 2025-06-26 12:38:04,548 calibrate.py _range_qc_combined_nc():916 [1] gps_time: deleting 10 values found outside of above ranges: ['2007-05-15T04:16:55.183884288' '2007-05-15T04:16:56.183815936' '2007-05-15T04:16:57.183747584' '2007-05-15T04:16:58.183678976' '2007-05-15T04:16:59.183610368' '2007-05-15T04:17:17.182377472' '2007-05-15T04:17:20.182172160' '2007-05-15T04:17:21.182103296' '2007-05-15T04:17:22.182034944' '2007-05-15T04:17:23.181966592'] INFO 2025-06-26 12:38:04,550 calibrate.py _range_qc_combined_nc():916 [1] gps_latitude: deleting 10 values found outside of above ranges: [65.02581717 65.019063 65.01232833 65.005611 64.9988955 64.877921 64.85776667 64.85105583 64.84435133 64.8376585 ] INFO 2025-06-26 12:38:04,551 calibrate.py _range_qc_combined_nc():916 [1] gps_longitude: deleting 10 values found outside of above ranges: [-96.93101867 -96.93535433 -96.939652 -96.94392783 -96.94820883 -97.0253135 -97.03815433 -97.042417 -97.04666033 -97.0509145 ] INFO 2025-06-26 12:38:04,555 calibrate.py _range_qc_combined_nc():936 [1] Done range checking gps INFO 2025-06-26 12:38:04,555 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 12:38:04,557 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:38:05,168 calibrate.py _nudge_pos():1806 [1] 83: 0.180 0.0000189 -0.0000172 47 0.16 17.173 -19.527 2007-05-14T22:01:45.995869440 INFO 2025-06-26 12:38:05,218 calibrate.py _nudge_pos():1806 [1] 88: 0.180 0.0001709 -0.0012264 16531 55.36 0.459 -4.105 2007-05-14T22:57:11.998022912 INFO 2025-06-26 12:38:05,923 calibrate.py _nudge_pos():1806 [1] 158: 0.180 -0.0011539 -0.0002780 15562 51.93 -3.301 -0.992 2007-05-14T23:50:17.999766528 INFO 2025-06-26 12:38:06,840 calibrate.py _nudge_pos():1806 [1] 248: 0.190 0.0004402 -0.0011411 15495 51.71 1.265 -4.089 2007-05-15T00:43:29.991100416 INFO 2025-06-26 12:38:07,352 calibrate.py _nudge_pos():1806 [1] 298: 0.180 -0.0012969 -0.0003549 15974 53.28 -3.617 -1.234 2007-05-15T01:37:35.998733568 INFO 2025-06-26 12:38:08,234 calibrate.py _nudge_pos():1806 [1] 384: 0.180 -0.0000267 -0.0000045 15 0.05 -84.874 -17.760 2007-05-15T01:39:03.992705536 INFO 2025-06-26 12:38:08,296 calibrate.py _nudge_pos():1806 [1] 390: 0.180 0.0004763 -0.0012315 15539 51.83 1.365 -4.403 2007-05-15T02:30:59.999244544 INFO 2025-06-26 12:38:08,911 calibrate.py _nudge_pos():1806 [1] 449: 0.190 -0.0021335 -0.0004637 16315 54.43 -5.824 -1.578 2007-05-15T03:26:23.991535360 INFO 2025-06-26 12:38:09,398 calibrate.py _nudge_pos():1806 [1] 496: 0.180 0.0005027 -0.0000794 15 0.05 1600.755 -315.171 2007-05-15T03:27:12.998178304 INFO 2025-06-26 12:38:09,532 calibrate.py _nudge_pos():1806 [1] 509: 0.190 0.0008859 -0.0001590 14988 49.98 2.633 -0.589 2007-05-15T04:17:24.991842560 INFO 2025-06-26 12:38:10,160 calibrate.py _nudge_pos():1806 [1] 569: 0.190 -0.0017596 -0.0008333 16570 55.26 -4.731 -2.794 2007-05-15T05:13:39.990639104 INFO 2025-06-26 12:38:10,893 calibrate.py _nudge_pos():1806 [1] 639: 0.180 0.0005395 -0.0012302 15259 50.88 1.575 -4.480 2007-05-15T06:05:41.996767232 INFO 2025-06-26 12:38:11,612 calibrate.py _nudge_pos():1806 [1] 707: 0.170 -0.0015618 -0.0008609 16214 54.08 -4.291 -2.950 2007-05-15T07:00:53.999879424 INFO 2025-06-26 12:38:12,091 calibrate.py _nudge_pos():1806 [1] 752: 0.180 0.0000002 0.0000181 35 0.11 0.316 29.610 2007-05-15T07:01:45.996317440 INFO 2025-06-26 12:38:12,113 calibrate.py _nudge_pos():1806 [1] 754: 0.180 0.0010699 -0.0014442 15679 52.31 3.038 -5.116 2007-05-15T07:54:05.991213056 INFO 2025-06-26 12:38:12,695 calibrate.py _nudge_pos():1806 [1] 809: 0.180 -0.0008539 0.0000517 15624 52.11 -2.434 0.184 2007-05-15T08:47:06.993299456 INFO 2025-06-26 12:38:13,526 calibrate.py _nudge_pos():1806 [1] 887: 0.180 0.0014289 -0.0012657 16158 53.90 3.939 -4.351 2007-05-15T09:42:17.996480256 INFO 2025-06-26 12:38:14,284 calibrate.py _nudge_pos():1806 [1] 958: 0.180 0.0000171 -0.0000011 30 0.10 26.270 -2.134 2007-05-15T09:43:33.991274240 INFO 2025-06-26 12:38:14,306 calibrate.py _nudge_pos():1806 [1] 960: 0.170 -0.0011004 -0.0007278 15414 51.41 -3.180 -2.623 2007-05-15T10:34:59.999868160 INFO 2025-06-26 12:38:14,868 calibrate.py _nudge_pos():1806 [1] 1013: 0.180 0.0018756 -0.0008784 16891 56.33 4.947 -2.890 2007-05-15T11:32:11.994760192 INFO 2025-06-26 12:38:15,437 calibrate.py _nudge_pos():1806 [1] 1066: 0.180 0.0000820 -0.0000288 15 0.05 261.183 -114.358 2007-05-15T11:33:06.990992896 INFO 2025-06-26 12:38:15,449 calibrate.py _nudge_pos():1806 [1] 1067: 0.180 -0.0009432 -0.0007003 14975 49.96 -2.805 -2.597 2007-05-15T12:23:04.995615488 INFO 2025-06-26 12:38:16,033 calibrate.py _nudge_pos():1806 [1] 1120: 0.180 0.0017347 -0.0018106 17008 56.73 4.543 -5.914 2007-05-15T13:20:41.998794496 INFO 2025-06-26 12:38:16,557 calibrate.py _nudge_pos():1806 [1] 1168: 0.180 -0.0009555 -0.0016020 15260 50.91 -2.788 -5.830 2007-05-15T14:12:23.996293120 INFO 2025-06-26 12:38:17,568 calibrate.py _nudge_pos():1806 [1] 1261: 0.180 0.0004888 -0.0008592 8535 28.46 2.551 -5.593 2007-05-15T14:42:23.992985088 INFO 2025-06-26 12:38:18,338 calibrate.py _nudge_pos():1806 [1] 1332: 0.180 0.0000293 -0.0000021 15 0.05 93.285 -8.345 2007-05-15T14:43:37.997915392 INFO 2025-06-26 12:38:18,371 calibrate.py _nudge_pos():1806 [1] 1335: 0.180 -0.0011440 -0.0005872 8284 27.63 -6.152 -3.938 2007-05-15T15:11:17.994197760 INFO 2025-06-26 12:38:18,581 calibrate.py _nudge_pos():1862 [1] 1323: - - - 4 0.01 - - INFO 2025-06-26 12:38:18,581 calibrate.py _nudge_pos():1868 [1] Points in final series = 308953 WARNING 2025-06-26 12:38:18,995 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 12:38:51,537 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:39:09,272 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:39:11,108 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:39:11,112 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.134.09/ctd1.nc INFO 2025-06-26 12:39:11,114 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:39:11,114 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 12:39:11,114 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:39:24,675 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:39:26,564 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:39:26,568 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.134.09/ctd2.nc INFO 2025-06-26 12:39:26,569 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 12:39:26,570 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 12:39:26,570 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:39:28,698 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:39:31,558 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3693606 3693607 3693608] INFO 2025-06-26 12:39:32,129 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:39:32,136 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 12:39:32,136 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.134.09 ERROR 2025-06-26 12:39:32,136 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.134.09 INFO 2025-06-26 12:39:32,188 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_cal.nc INFO 2025-06-26 12:39:51,383 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 12:39:51,388 process.py align():251 [1] Alignment steps for 2007.134.09 INFO 2025-06-26 12:39:51,426 align.py process_cal():139 [1] Processing dorado_2007.134.09_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.134.09 INFO 2025-06-26 12:39:51,547 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:39:51,558 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:39:51,774 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:39:51,789 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:39:51,978 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:39:51,990 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:39:52,110 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:39:52,110 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:39:52,192 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:39:52,204 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:39:52,389 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:52,398 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:52,559 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:52,568 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:52,731 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:52,740 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:52,909 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:52,917 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:53,084 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:53,093 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:53,252 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:53,261 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:53,423 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:53,433 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:53,593 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:53,602 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:53,764 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:53,773 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:53,937 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:53,946 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:54,124 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:54,133 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:54,299 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:54,308 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:54,472 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:54,480 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:54,644 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:54,653 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:54,817 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:54,826 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:54,990 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:55,001 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:55,164 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:55,173 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:55,335 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:55,345 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:55,509 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:55,518 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:55,682 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:39:55,691 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:39:55,890 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:39:56,014 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:39:56,140 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:39:56,278 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:39:56,420 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 12:39:56,457 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_align.nc INFO 2025-06-26 12:39:56,590 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 12:39:56,592 process.py resample():273 [1] Resampling steps for 2007.134.09 INFO 2025-06-26 12:39:56,593 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:39:56,626 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_align.nc mission netCDF file INFO 2025-06-26 12:39:56,634 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_align.nc mission netCDF file INFO 2025-06-26 12:39:56,636 resample.py get_mission_start_end():1145 [1] navigation: 2007-05-14T22:00:45.560009728 to 2007-05-15T15:11:36.792909824 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:39:56,639 resample.py get_mission_start_end():1145 [1] hs2 : 2007-05-14T22:00:18.711848704 to 2007-05-15T15:11:36.682917376 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 12:39:56,642 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-05-14T22:00:39.810403584 to 2007-05-15T15:11:36.692916992 (0 days 00:00:00.099992832 before mission_end) INFO 2025-06-26 12:39:56,644 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-05-14T22:00:40.490356992 to 2007-05-15T15:11:36.732913920 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 12:39:56,646 resample.py get_mission_start_end():1145 [1] isus : 2007-05-14T22:01:14.828004608 to 2007-05-15T15:11:35.752981248 (0 days 00:00:01.039928576 before mission_end) INFO 2025-06-26 12:39:56,648 resample.py get_mission_start_end():1145 [1] biolume : 2007-05-14T22:00:11.292322816 to 2007-05-15T15:11:36.122921472 (0 days 00:00:00.669988352 before mission_end) INFO 2025-06-26 12:39:56,650 resample.py get_mission_start_end():1145 [1] tailcone : 2007-05-14T22:00:15.652058368 to 2007-05-15T15:11:36.352940032 (0 days 00:00:00.439969792 before mission_end) INFO 2025-06-26 12:39:56,650 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_align.nc mission netCDF file INFO 2025-06-26 12:39:56,651 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,296 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,399 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,497 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,595 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,680 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,761 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,853 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:57,937 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,015 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,091 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,167 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,244 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,321 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,402 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,479 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,554 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,634 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,714 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,792 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,870 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:58,951 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:59,031 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:59,061 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:59,088 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:59,113 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:59,144 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:59,176 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:39:59,622 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_1S.nc INFO 2025-06-26 12:40:01,358 create_products.py gulper_odv():401 [1] No gulper times found for 2007.134.09 INFO 2025-06-26 12:40:01,359 process.py archive():337 [1] Archiving steps for 2007.134.09 INFO 2025-06-26 12:40:01,359 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09, BASE_PATH = /data/auv_data INFO 2025-06-26 12:40:01,360 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:40:01,362 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.09_1S.nc INFO 2025-06-26 12:40:01,406 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:40:01,407 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.09_cal.nc INFO 2025-06-26 12:40:01,625 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:40:01,626 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.09_align.nc INFO 2025-06-26 12:40:01,824 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:40:01,886 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:01,947 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:01,952 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:01,993 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:02,174 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:02,183 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:02,252 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:02,267 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:02,431 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.09 done. INFO 2025-06-26 12:40:02,432 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:40:02,432 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.09/dorado_2007.134.09_processing.log /Volumes/AUVCTD/surveys/2007/netcdf