INFO 2025-06-26 12:40:02,529 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 12:40:02,529 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - C1 to M2 & back - gulper tripped at nephaloid layers (we hope!) - ctdToUse = ctd1 INFO 2025-06-26 12:40:02,529 process.py process_mission():449 [1] Processing AUVCTD mission 2007.142.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:40:02,529 process.py download_process():165 [1] Download and processing steps for 2007.142.02 INFO 2025-06-26 12:40:02,529 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007142/2007.142.02 INFO 2025-06-26 12:40:02,529 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007142/2007.142.02 to /data/auv_data/dorado/missionlogs/2007.142.02 INFO 2025-06-26 12:40:09,383 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.142.02 INFO 2025-06-26 12:40:09,383 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/ctdDriver.log (25766179 bytes) INFO 2025-06-26 12:40:11,394 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.142.02/ctdDriver.log: [ 27 139 220 442 464 561 623 654 690 741 972 1009 1025 1067 1195 1489 1527 1530 1577 1778 2037 2234 2286 2333 2390 2414 2632 2773 3339 3535 3666 4829 4966 5113 5225 5330 5353 5543 6342 7230 7426 7499 7659 8367 9327 9592 9740 10346 10871 11269 11894 11940 12036 12596 14288 14465 14968 16271 17152 17437 18050 18942 19261 21094 21394 23738 23908 24272 25329 28501 29706 31268 31384 31693 32749 33069 35033 35824 38402 40578 43146 45618 49855 51146 52730 55759 56571 56978 57678 59844 60633 63081 64714 65988 66419 73885 74070 78086 80809 83431 86245 86613 86859 88298 90148 90307 93084 95630 97097 99473 100976 103865 104236 104716 108093 116751 117008 123086 123219 128469 129440 130076 135488 135587 137599 138067 138102 143880 145216 145601 149949 152334 153104 157314 158574 159448 166561 168103 170743 175340 177459 180788 183106 184174 187900 189251 189321 190888 195014 195268 198105 203449 205610 209243 209691 210964 213006 213111 215005 216359 219911 219912 220612 223471 224469 224774 224978 227266 230128 231187 235128 235616 244613 244813 250561 251329 251927 255050 256974 258044 258116 259042 264759 265614 271076 273267 274976 278189 280612 282944 283763 284076 288114 291997 292291] INFO 2025-06-26 12:40:11,493 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/ctdDriver2.log (25765029 bytes) INFO 2025-06-26 12:40:13,428 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.142.02/ctdDriver2.log: [ 4 27 220 443 465 562 624 655 691 741 973 1010 1026 1196 1528 1531 1578 1778 2037 2285 2332 2389 2413 2471 2631 2740 2773 3537 3668 4831 4968 5110 5222 5327 5349 5541 6339 7226 7422 7495 7503 7655 8363 9324 9446 9589 9737 10343 10868 11891 11937 12033 12592 14284 14461 16267 17147 17432 18045 18937 21086 21385 23730 23900 24264 25309 25321 28492 29697 31375 31684 32740 33060 35815 37960 38391 40567 41414 43135 44845 45608 46280 49845 51136 52720 55749 56561 56935 57669 59142 59835 60045 60624 63073 65979 66410 67293 73876 74061 78078 80767 83423 86236 86604 86851 88289 90139 93075 95620 97087 99463 100966 103571 104226 104706 107315 108083 115550 116743 117001 123078 123211 128428 129431 130068 135123 135480 135541 136577 137591 138059 143871 145207 145593 150585 152260 157305 159438 166120 166551 168094 170734 173664 175331 176095 177450 180780 183098 184166 187892 189313 190881 195007 195262 199930 205601 209234 209682 210956 211299 212998 213103 214996 216350 219903 220603 223462 224460 227256 230118 231177 235118 235606 240332 243103 244603 244803 247965 251917 255040 258034 258105 259030 264747 265602 271065 273256 278177 280600 282932 283751 284063 288101 291385 291984 292279] INFO 2025-06-26 12:40:13,545 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/gps.log (126284 bytes) INFO 2025-06-26 12:40:13,571 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/hydroscatlog.log (17568374 bytes) INFO 2025-06-26 12:40:15,672 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.142.02/hydroscatlog.log: [ 1 3 4 5 28 37 74 88 104 225 315 412 548 739 825 833 835 902 1074 1096 1111 1577 1618 1866 1914 2125 2375 2422 2649 2830 3323 3430 3432 3627 3964 3965 4275 4899 5000 5102 5426 5449 5640 6284 6389 6439 7327 7347 7595 7596 7603 7615 7616 7757 8463 9424 9836 10443 10970 11306 11370 11402 11997 12697 14389 14567 14879 17259 17545 18157 19050 19368 23082 23096 23139 24376 25495 25672 29811 31490 31799 32853 33173 35889 35928 38075 38100 38609 40682 41682 44960 45722 45723 49304 49962 50495 51253 52835 55682 57085 57785 59951 66093 67062 69804 70106 73236 73986 76817 78187 80910 83532 85682 86712 86958 93180 95725 96552 96959 98328 99566 100679 102618 103672 104325 104806 107414 107415 108189 109729 110385 115645 117094 117650 123169 123302 127888 128515 128549 130524 130674 135566 135627 135628 136661 137238 137675 138143 138179 145288 145673 148398 150665 152372 152402 153173 160668 164092 166622 166623 168165 170803 173140 176162 176778 178094 179085 180085 183162 184229 189372 190940 195319 197653 199157 199519 199986 202177 205655 209285 209733 211007 211079 213152 215045 215242 220648 223796 223832 228150 230160 230257 230620 237728 240368 244637 247650 247999 251352 251949 255070 256992 258062 258134 258912 259060 264773 265628 271472 273278 278198 280620 282952 284084 284909 289732 291623 292000 292292] INFO 2025-06-26 12:40:15,747 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/navigation.log (86291874 bytes) INFO 2025-06-26 12:40:22,552 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/isuslog.log (1642997 bytes) INFO 2025-06-26 12:40:22,727 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/parosci.log (30809606 bytes) INFO 2025-06-26 12:40:25,403 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/tailCone.log (3551659 bytes) INFO 2025-06-26 12:40:25,862 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.142.02/biolume.log (19927404 bytes) INFO 2025-06-26 12:40:27,823 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:40:28,940 logs2netcdfs.py download_process_logs():807 [1] Time to process: 19.56 seconds WARNING 2025-06-26 12:40:28,941 process.py download_process():196 [1] No lopc.bin file for 2007.142.02 INFO 2025-06-26 12:40:28,941 process.py calibrate():227 [1] Calibration steps for 2007.142.02 INFO 2025-06-26 12:40:29,526 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 12:40:29,528 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:40:30,323 calibrate.py _nudge_pos():1806 [1] 101: 0.150 0.0000045 -0.0000077 25 0.08 8.334 -17.923 2007-05-22T18:50:27.483184896 INFO 2025-06-26 12:40:30,353 calibrate.py _nudge_pos():1806 [1] 104: 0.140 0.0002718 -0.0014778 3290 11.10 3.636 -24.676 2007-05-22T19:01:35.487423488 INFO 2025-06-26 12:40:31,042 calibrate.py _nudge_pos():1806 [1] 171: 0.150 -0.0015598 -0.0022546 14546 48.70 -4.756 -8.579 2007-05-22T19:51:23.482731776 INFO 2025-06-26 12:40:31,666 calibrate.py _nudge_pos():1806 [1] 232: 0.150 0.0030182 -0.0045059 11199 37.38 11.990 -22.337 2007-05-22T20:29:47.484896768 INFO 2025-06-26 12:40:31,697 calibrate.py _nudge_pos():1806 [1] 235: 0.150 0.0000022 -0.0000038 15 0.05 7.033 -15.277 2007-05-22T20:29:52.484554240 INFO 2025-06-26 12:40:31,884 calibrate.py _nudge_pos():1806 [1] 253: 0.150 -0.0000076 -0.0000065 15 0.05 -24.082 -25.644 2007-05-22T20:30:12.483184384 INFO 2025-06-26 12:40:32,558 calibrate.py _nudge_pos():1806 [1] 319: 0.140 -0.0005715 -0.0016293 15516 51.78 -1.639 -5.831 2007-05-22T21:23:05.485818624 INFO 2025-06-26 12:40:33,220 calibrate.py _nudge_pos():1806 [1] 384: 0.150 0.0006155 -0.0055490 11539 38.51 2.373 -26.698 2007-05-22T22:02:41.483051776 INFO 2025-06-26 12:40:33,796 calibrate.py _nudge_pos():1806 [1] 439: 0.150 -0.0000679 0.0001144 15 0.05 -216.216 454.190 2007-05-22T22:03:38.479147264 INFO 2025-06-26 12:40:33,881 calibrate.py _nudge_pos():1806 [1] 447: 0.150 0.0029786 -0.0031447 13376 44.63 9.913 -13.056 2007-05-22T22:48:23.485211648 INFO 2025-06-26 12:40:34,006 calibrate.py _nudge_pos():1806 [1] 459: 0.160 -0.0000504 0.0000048 25 0.08 -93.579 11.054 2007-05-22T22:48:39.484115712 INFO 2025-06-26 12:40:34,414 calibrate.py _nudge_pos():1806 [1] 498: 0.150 0.0000187 -0.0000526 30 0.10 28.689 -100.847 2007-05-22T22:49:23.481101824 INFO 2025-06-26 12:40:34,551 calibrate.py _nudge_pos():1806 [1] 511: 0.150 0.0036292 0.0016780 16184 54.00 9.984 5.758 2007-05-22T23:43:35.478324736 INFO 2025-06-26 12:40:34,605 calibrate.py _nudge_pos():1806 [1] 516: 0.150 0.0001154 -0.0000470 100 0.33 51.930 -26.369 2007-05-22T23:43:59.486680064 INFO 2025-06-26 12:40:35,399 calibrate.py _nudge_pos():1806 [1] 592: 0.140 0.0014358 -0.0066730 14315 47.75 4.467 -25.897 2007-05-23T00:32:59.485276160 INFO 2025-06-26 12:40:36,135 calibrate.py _nudge_pos():1806 [1] 662: 0.140 0.0029264 -0.0021716 14551 48.55 8.956 -8.289 2007-05-23T01:22:41.480995584 INFO 2025-06-26 12:40:37,192 calibrate.py _nudge_pos():1806 [1] 762: 0.140 0.0000378 0.0000655 35 0.11 49.504 107.143 2007-05-23T01:24:28.483665408 INFO 2025-06-26 12:40:37,213 calibrate.py _nudge_pos():1806 [1] 764: 0.140 0.0012421 0.0037685 15796 52.70 3.502 13.251 2007-05-23T02:17:11.486984704 INFO 2025-06-26 12:40:37,256 calibrate.py _nudge_pos():1806 [1] 768: 0.140 0.0000409 -0.0000461 140 0.46 13.106 -18.439 2007-05-23T02:17:42.484861440 INFO 2025-06-26 12:40:37,690 calibrate.py _nudge_pos():1806 [1] 808: 0.140 0.0023566 -0.0016609 14426 48.11 7.278 -6.397 2007-05-23T03:06:29.484348160 INFO 2025-06-26 12:40:38,331 calibrate.py _nudge_pos():1806 [1] 868: 0.140 0.0044609 0.0037869 22303 74.43 8.904 9.428 2007-05-23T04:21:54.484364288 INFO 2025-06-26 12:40:38,533 calibrate.py _nudge_pos():1806 [1] 887: 0.140 0.0000111 0.0000262 20 0.06 26.089 76.720 2007-05-23T04:22:16.482857472 INFO 2025-06-26 12:40:38,735 calibrate.py _nudge_pos():1806 [1] 906: 0.140 -0.0000127 -0.0001169 25 0.08 -23.594 -270.714 2007-05-23T04:22:39.481282048 INFO 2025-06-26 12:40:38,831 calibrate.py _nudge_pos():1806 [1] 915: 0.140 0.0050320 0.0030204 23612 78.78 9.488 7.104 2007-05-23T05:41:34.486911744 INFO 2025-06-26 12:40:39,564 calibrate.py _nudge_pos():1806 [1] 981: 0.130 0.0045393 0.0014331 17401 58.03 11.618 4.576 2007-05-23T06:40:41.483925760 INFO 2025-06-26 12:40:39,653 calibrate.py _nudge_pos():1806 [1] 989: 0.140 -0.0003152 0.0003645 30 0.10 -484.255 698.741 2007-05-23T06:40:54.483035392 INFO 2025-06-26 12:40:40,162 calibrate.py _nudge_pos():1806 [1] 1035: 0.140 0.0000043 0.0000087 15 0.05 13.570 34.366 2007-05-23T06:41:42.479747328 INFO 2025-06-26 12:40:40,263 calibrate.py _nudge_pos():1806 [1] 1044: 0.130 0.0014551 0.0002271 7447 24.85 8.698 1.694 2007-05-23T07:06:41.487058432 INFO 2025-06-26 12:40:40,779 calibrate.py _nudge_pos():1806 [1] 1092: 0.140 0.0007145 0.0000883 4347 14.50 7.320 1.129 2007-05-23T07:21:59.484171264 INFO 2025-06-26 12:40:40,790 calibrate.py _nudge_pos():1806 [1] 1093: 0.130 -0.0000413 0.0000258 110 0.36 -16.895 13.148 2007-05-23T07:22:21.482664192 INFO 2025-06-26 12:40:41,133 calibrate.py _nudge_pos():1806 [1] 1124: 0.140 -0.0001321 0.0002501 25 0.08 -245.202 579.276 2007-05-23T07:22:56.480266496 INFO 2025-06-26 12:40:41,325 calibrate.py _nudge_pos():1806 [1] 1142: 0.140 0.0033381 0.0003742 14648 48.85 10.149 1.420 2007-05-23T08:12:04.478314752 INFO 2025-06-26 12:40:42,054 calibrate.py _nudge_pos():1806 [1] 1207: 0.140 0.0022079 -0.0006180 12000 40.05 8.187 -2.860 2007-05-23T08:53:11.479313920 INFO 2025-06-26 12:40:42,550 calibrate.py _nudge_pos():1806 [1] 1253: 0.140 0.0023709 -0.0012586 15606 52.05 6.764 -4.481 2007-05-23T09:45:59.482290688 INFO 2025-06-26 12:40:43,251 calibrate.py _nudge_pos():1806 [1] 1316: 0.130 0.0014428 -0.0009433 12009 40.06 5.347 -4.363 2007-05-23T10:27:05.483358208 INFO 2025-06-26 12:40:43,856 calibrate.py _nudge_pos():1806 [1] 1370: 0.130 0.0021954 -0.0010448 15835 52.81 6.171 -3.666 2007-05-23T11:20:47.482636032 INFO 2025-06-26 12:40:44,460 calibrate.py _nudge_pos():1806 [1] 1424: 0.130 0.0021346 0.0002604 11998 40.01 7.919 1.206 2007-05-23T12:01:41.484525568 INFO 2025-06-26 12:40:45,006 calibrate.py _nudge_pos():1806 [1] 1473: 0.130 0.0021379 0.0006240 14298 47.70 6.653 2.424 2007-05-23T12:50:11.485176832 INFO 2025-06-26 12:40:45,087 calibrate.py _nudge_pos():1806 [1] 1480: 0.130 0.0002973 -0.0000989 40 0.13 339.449 -141.016 2007-05-23T12:50:25.484217600 INFO 2025-06-26 12:40:45,592 calibrate.py _nudge_pos():1806 [1] 1525: 0.130 0.0005190 -0.0000903 4960 16.53 4.660 -1.013 2007-05-23T13:07:41.483246848 INFO 2025-06-26 12:40:46,214 calibrate.py _nudge_pos():1806 [1] 1580: 0.140 0.0005002 0.0001658 12499 41.70 1.780 0.737 2007-05-23T13:50:17.478149120 INFO 2025-06-26 12:40:46,826 calibrate.py _nudge_pos():1806 [1] 1635: 0.130 0.0007281 0.0002569 9865 32.90 3.284 1.447 2007-05-23T14:24:05.479221504 INFO 2025-06-26 12:40:47,477 calibrate.py _nudge_pos():1806 [1] 1692: 0.120 0.0015096 0.0000930 13058 43.56 5.142 0.396 2007-05-23T15:08:35.486313472 INFO 2025-06-26 12:40:48,035 calibrate.py _nudge_pos():1862 [1] 1709: - - - 5 0.01 - - INFO 2025-06-26 12:40:48,036 calibrate.py _nudge_pos():1868 [1] Points in final series = 365634 WARNING 2025-06-26 12:40:48,590 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 12:41:25,171 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 12 of 292572 INFO 2025-06-26 12:41:27,408 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:41:48,332 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:41:50,514 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:41:50,518 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.142.02/ctd1.nc INFO 2025-06-26 12:41:50,520 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 12:41:50,520 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 12:41:50,520 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:42:06,691 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:42:08,918 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:42:08,922 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.142.02/ctd2.nc INFO 2025-06-26 12:42:08,924 calibrate.py _range_qc_combined_nc():898 [1] Setting 166 ctd2_salinity values to NaN INFO 2025-06-26 12:42:08,925 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 12:42:08,925 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:42:09,025 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:42:12,490 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4387684 4387685 4387686] INFO 2025-06-26 12:42:13,150 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:42:13,157 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 12:42:13,158 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.142.02 ERROR 2025-06-26 12:42:13,158 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.142.02 INFO 2025-06-26 12:42:13,217 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_cal.nc INFO 2025-06-26 12:42:36,030 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 12:42:36,035 process.py align():251 [1] Alignment steps for 2007.142.02 INFO 2025-06-26 12:42:36,077 align.py process_cal():139 [1] Processing dorado_2007.142.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.142.02 INFO 2025-06-26 12:42:36,169 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:42:36,178 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:42:36,420 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:42:36,435 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:42:36,657 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:42:36,669 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:42:36,806 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:42:36,806 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:42:36,901 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:42:36,914 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:42:37,129 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:37,140 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:42:37,329 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:37,340 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:42:37,540 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:37,550 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:42:37,740 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:37,750 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:37,944 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:37,955 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:38,145 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:38,156 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:38,348 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:38,359 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:38,558 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:38,568 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:38,760 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:38,771 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:38,962 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:38,972 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:39,168 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:39,178 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:39,368 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:39,378 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:39,570 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:39,580 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:39,771 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:39,781 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:39,973 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:39,983 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:40,179 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:40,193 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:40,389 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:40,400 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:40,595 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:40,605 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:40,797 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:40,807 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:41,000 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.142.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:42:41,010 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:42:41,243 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:42:41,388 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:42:41,533 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.70 INFO 2025-06-26 12:42:41,682 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:42:41,838 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 12:42:41,880 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_align.nc INFO 2025-06-26 12:42:42,028 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 12:42:42,031 process.py resample():273 [1] Resampling steps for 2007.142.02 INFO 2025-06-26 12:42:42,031 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:42:42,064 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_align.nc mission netCDF file INFO 2025-06-26 12:42:42,073 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_align.nc mission netCDF file INFO 2025-06-26 12:42:42,075 resample.py get_mission_start_end():1145 [1] navigation: 2007-05-22T18:49:15.778096896 to 2007-05-23T15:09:25.482888704 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:42:42,078 resample.py get_mission_start_end():1145 [1] hs2 : 2007-05-22T18:48:50.239846400 to 2007-05-23T15:09:25.422892800 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 12:42:42,081 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-05-22T18:49:10.858434048 to 2007-05-23T15:09:25.462890240 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 12:42:42,083 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-05-22T18:49:11.138414848 to 2007-05-23T15:09:25.322899456 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 12:42:42,085 resample.py get_mission_start_end():1145 [1] isus : 2007-05-22T18:49:59.475103744 to 2007-05-23T15:09:24.612948224 (0 days 00:00:00.869940480 before mission_end) INFO 2025-06-26 12:42:42,087 resample.py get_mission_start_end():1145 [1] biolume : 2007-05-22T18:48:42.360352000 to 2007-05-23T15:09:24.522920192 (0 days 00:00:00.959968512 before mission_end) INFO 2025-06-26 12:42:42,088 resample.py get_mission_start_end():1145 [1] tailcone : 2007-05-22T18:48:46.200123392 to 2007-05-23T15:09:24.792935936 (0 days 00:00:00.689952768 before mission_end) INFO 2025-06-26 12:42:42,089 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_align.nc mission netCDF file INFO 2025-06-26 12:42:42,090 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:42,806 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:42,922 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,036 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,150 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,247 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,342 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,438 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,532 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,623 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,715 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,804 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,894 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:43,984 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,076 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,165 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,254 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,346 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,438 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,535 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,628 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,721 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,813 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,847 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,878 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,905 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,939 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:44,974 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:42:45,487 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_1S.nc INFO 2025-06-26 12:42:48,972 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 12:42:58,492 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.142.02/dorado_2007.142.02_1S_Gulper.txt INFO 2025-06-26 12:42:58,492 process.py archive():337 [1] Archiving steps for 2007.142.02 INFO 2025-06-26 12:42:58,492 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02, BASE_PATH = /data/auv_data INFO 2025-06-26 12:42:58,493 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:42:58,494 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.142.02_1S.nc INFO 2025-06-26 12:42:58,546 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:42:58,547 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.142.02_cal.nc INFO 2025-06-26 12:42:58,803 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:42:58,804 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.142.02_align.nc INFO 2025-06-26 12:42:59,042 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:42:59,112 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,181 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,186 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,232 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,437 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,447 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,536 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,553 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,740 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007142/2007.142.02 done. INFO 2025-06-26 12:42:59,740 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:42:59,741 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.142.02_1S_Gulper.txt INFO 2025-06-26 12:42:59,746 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.142.02/dorado_2007.142.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 12:42:59,746 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.142.02/dorado_2007.142.02_processing.log /Volumes/AUVCTD/surveys/2007/netcdf