INFO 2025-06-26 12:58:00,767 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 12:58:00,768 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Canyon Axis - ctdToUse = ctd1 INFO 2025-06-26 12:58:00,768 process.py process_mission():449 [1] Processing AUVCTD mission 2007.234.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:58:00,768 process.py download_process():165 [1] Download and processing steps for 2007.234.05 INFO 2025-06-26 12:58:00,768 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007234/2007.234.05 INFO 2025-06-26 12:58:00,768 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007234/2007.234.05 to /data/auv_data/dorado/missionlogs/2007.234.05 INFO 2025-06-26 12:58:07,218 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.234.05 INFO 2025-06-26 12:58:07,218 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/ctdDriver.log (25302419 bytes) INFO 2025-06-26 12:58:08,978 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.234.05/ctdDriver.log: [ 7 29 148 470 693 753 812 826 918 1009 1494 1521 1535 1566 1622 1772 2028 2166 2241 2380 2816 2924 3091 3184 3288 3565 4687 4947 5119 5148 5343 6079 6602 6807 7401 8234 9093 9985 10715 10953 11129 11263 11457 12244 13613 13742 16893 19065 19119 21583 23891 24267 24763 24985 26894 27643 28593 29203 31381 35286 37201 37849 39176 39595 40666 43848 46187 46587 52712 52805 56638 57828 58716 59822 61092 66740 66936 70033 70766 71621 72228 74051 76207 79150 80752 86648 88043 90564 94177 95384 96393 100889 102494 107601 108094 108387 108423 109605 111172 112521 114316 116719 121031 122678 123832 128877 131375 131660 132012 139254 141174 145516 146648 146664 152284 153744 154604 159395 161317 168032 171769 174746 174910 176671 177060 180734 181462 184171 184519 185894 188704 190237 194890 194960 201606 202074 206673 209186 210647 220850 221754 222022 223418 223835 226214 227194 229180 230534 231046 232370 233548 235187 237027 241263 244182 244761 248617 252571 255335 259187 261493 271906 272772 273218 274188 275480 281690 282195 287044 287415] INFO 2025-06-26 12:58:09,051 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/ctdDriver2.log (25301533 bytes) INFO 2025-06-26 12:58:10,890 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.234.05/ctdDriver2.log: [ 3 23 142 335 465 575 689 745 808 822 914 1005 1518 1562 1618 1768 2024 2161 2376 2813 2921 3088 3180 3283 3409 4339 4685 4945 5117 5137 5147 5256 5341 6077 6600 6805 7401 7703 8235 9093 10364 10713 10785 11128 11304 11458 12245 13615 13744 16899 16900 17334 19128 21593 24274 24992 25847 26899 27648 29208 31387 34139 35290 37205 37854 38975 39181 40479 40672 41426 43851 49184 52697 57067 57815 58702 59809 61078 62789 64130 66920 70016 70749 71605 72212 74036 77598 79137 80739 86637 87022 87455 88033 94168 95376 96912 102488 107595 108088 108417 109600 111168 114311 116712 121024 122671 123824 124151 131366 131651 132003 139120 141166 146639 146655 148794 152276 153736 154596 158120 161308 168023 171763 173615 174741 174803 174904 176665 177054 180727 181454 181947 184163 184510 188168 188694 190227 191668 194882 194952 201600 202069 206668 209180 210639 220841 221745 222013 223410 223656 223828 226207 229172 229611 230527 232365 235181 241257 244174 244753 248609 251485 251865 252563 253441 255327 258614 261486 266679 272762 273207 274177 275470 279743 281678 282183 287033 287404] INFO 2025-06-26 12:58:10,974 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/gps.log (133988 bytes) INFO 2025-06-26 12:58:10,996 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/hydroscatlog.log (17258414 bytes) INFO 2025-06-26 12:58:13,034 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.234.05/hydroscatlog.log: [ 3 22 102 110 228 302 326 421 552 618 826 839 898 899 912 936 1004 1096 1299 1315 1502 1584 1611 1656 1657 1947 2188 2257 2332 2388 2473 2474 2819 2826 2911 3019 3187 3280 3443 3511 3527 3528 3549 3666 4164 4441 4788 4985 5222 5242 5253 5362 5572 6185 6492 6708 6913 7509 7626 7813 7845 8343 8344 9697 10475 10895 11063 11373 11374 11416 11570 11668 12043 12357 12523 13728 15303 16267 16592 16791 17273 17447 18509 18824 19187 20451 21706 22376 22989 24013 24390 24887 25143 26106 26752 27022 27737 27771 29330 33836 33885 34261 34923 35415 36734 37328 37976 38624 39332 39725 40798 41551 41777 43022 43979 45473 45739 46722 51812 52851 52852 52945 55982 57972 58859 61234 61235 62946 63490 64287 66882 67485 70174 70908 71763 71791 72369 76348 77742 80894 83971 87175 87609 87985 88415 90707 94319 95527 97061 97644 98253 101032 102638 107742 107743 108529 108563 108566 109296 109749 110613 114458 114459 116796 118924 121171 121172 122819 124298 124688 131082 131798 132148 132191 134436 139265 139390 141309 145648 146781 146797 147113 148936 151703 154737 158259 161446 161741 162141 162195 166636 167066 169298 169946 170209 174876 174938 174939 175040 176799 177188 180151 180860 181588 182082 184644 186019 187112 187113 188301 190362 191802 192096 195015 195085 199296 200572 201029 201729 202198 208440 209307 209840 210767 210768 212288 214295 215158 220714 221791 221870 223535 223781 223953 226332 229296 229735 230651 231853 232487 232488 233665 233666 236798 237766 242018 242897 251985 253561 255447 255448 258734 259101 259298 261604 262161 262675 266212 267081 268874 272012 274295 277383 279860 280432 281139 281319 281795 282300 282484 287519 287546] INFO 2025-06-26 12:58:13,090 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/navigation.log (84754098 bytes) INFO 2025-06-26 12:58:19,178 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/isuslog.log (1702133 bytes) INFO 2025-06-26 12:58:19,347 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/parosci.log (29847206 bytes) INFO 2025-06-26 12:58:21,887 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/tailCone.log (3489979 bytes) INFO 2025-06-26 12:58:22,420 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.234.05/biolume.log (19575708 bytes) INFO 2025-06-26 12:58:24,345 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:58:25,332 logs2netcdfs.py download_process_logs():807 [1] Time to process: 18.11 seconds WARNING 2025-06-26 12:58:25,333 process.py download_process():196 [1] No lopc.bin file for 2007.234.05 INFO 2025-06-26 12:58:25,333 process.py calibrate():227 [1] Calibration steps for 2007.234.05 INFO 2025-06-26 12:58:25,806 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 12:58:25,808 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:58:26,718 calibrate.py _nudge_pos():1806 [1] 113: 0.020 0.0007343 -0.0000626 3764 12.73 8.563 -0.911 2007-08-22T21:37:42.098479872 INFO 2025-06-26 12:58:26,729 calibrate.py _nudge_pos():1806 [1] 114: 0.030 0.0000375 -0.0000270 60 0.20 28.344 -25.457 2007-08-22T21:37:54.097657600 INFO 2025-06-26 12:58:27,309 calibrate.py _nudge_pos():1806 [1] 171: 0.020 0.0020307 0.0014668 15174 50.76 5.939 5.354 2007-08-22T22:29:36.105155584 INFO 2025-06-26 12:58:27,817 calibrate.py _nudge_pos():1806 [1] 220: 0.030 0.0031827 0.0017780 12003 40.10 11.786 8.217 2007-08-22T23:10:30.097045760 INFO 2025-06-26 12:58:28,312 calibrate.py _nudge_pos():1806 [1] 267: 0.030 -0.0000401 0.0000017 40 0.13 -45.775 2.486 2007-08-22T23:11:24.103346176 INFO 2025-06-26 12:58:28,513 calibrate.py _nudge_pos():1806 [1] 284: 0.030 0.0000121 -0.0000208 15 0.05 38.528 -82.605 2007-08-22T23:11:43.102044672 INFO 2025-06-26 12:58:28,587 calibrate.py _nudge_pos():1806 [1] 291: 0.030 -0.0000115 -0.0000020 20 0.06 -27.015 -5.935 2007-08-22T23:11:53.101359616 INFO 2025-06-26 12:58:28,619 calibrate.py _nudge_pos():1806 [1] 294: 0.040 0.0002393 -0.0003678 16379 54.68 0.650 -1.247 2007-08-23T00:06:36.096459008 INFO 2025-06-26 12:58:28,998 calibrate.py _nudge_pos():1806 [1] 330: 0.030 -0.0000504 0.0000102 20 0.06 -118.260 29.901 2007-08-23T00:07:15.103786752 INFO 2025-06-26 12:58:29,127 calibrate.py _nudge_pos():1806 [1] 342: 0.030 -0.0000055 -0.0000016 15 0.05 -17.507 -6.423 2007-08-23T00:07:29.102827776 INFO 2025-06-26 12:58:29,315 calibrate.py _nudge_pos():1806 [1] 360: 0.030 -0.0013543 -0.0000004 11368 37.93 -5.303 -0.002 2007-08-23T00:45:42.105746176 INFO 2025-06-26 12:58:29,869 calibrate.py _nudge_pos():1806 [1] 412: 0.040 0.0000054 0.0000095 20 0.06 12.557 27.813 2007-08-23T00:46:37.101978880 INFO 2025-06-26 12:58:29,985 calibrate.py _nudge_pos():1806 [1] 423: 0.040 0.0025055 0.0013832 12607 42.06 8.847 6.094 2007-08-23T01:28:51.098388224 INFO 2025-06-26 12:58:30,552 calibrate.py _nudge_pos():1806 [1] 476: 0.040 0.0000363 -0.0000038 20 0.06 85.107 -11.158 2007-08-23T01:29:48.104482816 INFO 2025-06-26 12:58:30,648 calibrate.py _nudge_pos():1806 [1] 485: 0.040 -0.0000300 -0.0000175 25 0.08 -55.654 -40.436 2007-08-23T01:30:01.103592448 INFO 2025-06-26 12:58:30,691 calibrate.py _nudge_pos():1806 [1] 489: 0.050 0.0009665 0.0021933 17683 59.01 2.433 6.887 2007-08-23T02:29:05.100812032 INFO 2025-06-26 12:58:31,169 calibrate.py _nudge_pos():1806 [1] 534: 0.050 -0.0000585 -0.0000908 135 0.45 -19.455 -37.671 2007-08-23T02:30:17.105879296 INFO 2025-06-26 12:58:31,180 calibrate.py _nudge_pos():1806 [1] 535: 0.060 0.0016395 -0.0017141 14563 48.58 5.013 -6.538 2007-08-23T03:18:52.096188672 INFO 2025-06-26 12:58:31,607 calibrate.py _nudge_pos():1806 [1] 575: 0.060 -0.0006454 -0.0005997 14731 49.15 -1.951 -2.261 2007-08-23T04:08:42.101359360 INFO 2025-06-26 12:58:32,035 calibrate.py _nudge_pos():1806 [1] 615: 0.070 -0.0002786 -0.0000397 30 0.10 -428.241 -76.070 2007-08-23T04:09:27.098276864 INFO 2025-06-26 12:58:32,281 calibrate.py _nudge_pos():1806 [1] 638: 0.060 0.0018252 0.0043049 16598 55.36 4.898 14.408 2007-08-23T05:05:12.099128832 INFO 2025-06-26 12:58:32,726 calibrate.py _nudge_pos():1806 [1] 679: 0.070 0.0002864 0.0001532 15 0.05 911.834 608.297 2007-08-23T05:05:55.096183296 INFO 2025-06-26 12:58:32,912 calibrate.py _nudge_pos():1806 [1] 696: 0.060 0.0061003 -0.0028856 11756 39.21 23.115 -13.636 2007-08-23T05:45:24.103895040 INFO 2025-06-26 12:58:33,792 calibrate.py _nudge_pos():1806 [1] 774: 0.080 0.0089769 -0.0013395 16881 56.31 23.684 -4.408 2007-08-23T06:43:00.097143296 INFO 2025-06-26 12:58:34,501 calibrate.py _nudge_pos():1806 [1] 839: 0.080 0.0077892 -0.0009182 16827 56.13 20.616 -3.031 2007-08-23T07:40:12.102034688 INFO 2025-06-26 12:58:35,120 calibrate.py _nudge_pos():1806 [1] 894: 0.080 0.0064970 -0.0006619 16819 56.10 17.204 -2.187 2007-08-23T08:37:12.097748992 INFO 2025-06-26 12:58:35,753 calibrate.py _nudge_pos():1806 [1] 951: 0.080 0.0000332 -0.0000700 45 0.15 33.642 -88.470 2007-08-23T08:38:17.103295744 INFO 2025-06-26 12:58:35,804 calibrate.py _nudge_pos():1806 [1] 955: 0.080 0.0054437 0.0002226 16804 56.06 14.422 0.736 2007-08-23T09:34:24.102640640 INFO 2025-06-26 12:58:36,563 calibrate.py _nudge_pos():1806 [1] 1023: 0.090 0.0005518 -0.0002117 4193 13.98 5.862 -2.806 2007-08-23T09:49:30.100575488 INFO 2025-06-26 12:58:37,243 calibrate.py _nudge_pos():1806 [1] 1085: 0.090 0.0024144 0.0011177 15818 52.78 6.793 3.924 2007-08-23T10:43:18.099442432 INFO 2025-06-26 12:58:37,838 calibrate.py _nudge_pos():1806 [1] 1139: 0.100 0.0009027 0.0003859 10140 33.81 3.964 2.115 2007-08-23T11:18:00.096815872 INFO 2025-06-26 12:58:38,500 calibrate.py _nudge_pos():1806 [1] 1198: 0.100 0.0021369 0.0006922 16731 55.83 5.683 2.297 2007-08-23T12:14:48.103351296 INFO 2025-06-26 12:58:39,062 calibrate.py _nudge_pos():1806 [1] 1248: 0.100 0.0009091 0.0003121 9706 32.38 4.168 1.786 2007-08-23T12:48:00.096890368 INFO 2025-06-26 12:58:39,714 calibrate.py _nudge_pos():1806 [1] 1306: 0.110 0.0007972 0.0007719 16433 54.85 2.158 2.608 2007-08-23T13:43:48.097536768 INFO 2025-06-26 12:58:40,331 calibrate.py _nudge_pos():1806 [1] 1359: 0.110 0.0010557 0.0007230 10474 34.93 4.486 3.836 2007-08-23T14:19:36.100388608 INFO 2025-06-26 12:58:40,971 calibrate.py _nudge_pos():1806 [1] 1415: 0.110 0.0005608 0.0003289 13559 45.25 1.840 1.347 2007-08-23T15:05:46.100630528 INFO 2025-06-26 12:58:41,598 calibrate.py _nudge_pos():1806 [1] 1470: 0.110 0.0003055 -0.0001361 7023 23.43 1.935 -1.076 2007-08-23T15:30:06.100613632 INFO 2025-06-26 12:58:42,220 calibrate.py _nudge_pos():1806 [1] 1524: 0.110 0.0014606 -0.0003293 11845 39.51 5.486 -1.544 2007-08-23T16:10:30.104558080 INFO 2025-06-26 12:58:42,909 calibrate.py _nudge_pos():1806 [1] 1584: 0.120 0.0006651 0.0001997 7530 25.11 3.930 1.474 2007-08-23T16:36:36.097280256 INFO 2025-06-26 12:58:43,454 calibrate.py _nudge_pos():1806 [1] 1632: 0.110 0.0000213 -0.0000017 20 0.06 49.914 -4.833 2007-08-23T16:37:27.103785984 INFO 2025-06-26 12:58:43,477 calibrate.py _nudge_pos():1806 [1] 1634: 0.120 0.0008691 0.0002254 12361 41.23 3.128 1.013 2007-08-23T17:18:42.104236800 INFO 2025-06-26 12:58:45,971 calibrate.py _nudge_pos():1862 [1] 1815: - - - 4 0.01 - - INFO 2025-06-26 12:58:45,971 calibrate.py _nudge_pos():1868 [1] Points in final series = 359117 WARNING 2025-06-26 12:58:46,527 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 12:59:24,971 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:59:45,435 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:59:47,749 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:59:47,754 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.234.05/ctd1.nc INFO 2025-06-26 12:59:47,756 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:59:47,757 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 12:59:47,757 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:00:04,017 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:00:06,269 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:00:06,273 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.234.05/ctd2.nc INFO 2025-06-26 13:00:06,275 calibrate.py _range_qc_combined_nc():898 [1] Setting 165 ctd2_salinity values to NaN INFO 2025-06-26 13:00:06,276 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 13:00:06,276 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:00:06,377 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:00:09,874 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4316404 4316405 4316406] INFO 2025-06-26 13:00:10,565 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:00:10,573 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 13:00:10,574 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.234.05 ERROR 2025-06-26 13:00:10,574 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.234.05 INFO 2025-06-26 13:00:10,638 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_cal.nc INFO 2025-06-26 13:00:34,552 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 13:00:34,561 process.py align():251 [1] Alignment steps for 2007.234.05 INFO 2025-06-26 13:00:34,624 align.py process_cal():139 [1] Processing dorado_2007.234.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.234.05 INFO 2025-06-26 13:00:34,729 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:00:34,741 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:00:34,998 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:00:35,014 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:00:35,268 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:00:35,284 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:00:35,433 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:00:35,433 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:00:35,531 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:00:35,547 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:00:35,788 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:35,803 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:00:36,031 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:36,044 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:00:36,263 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:36,276 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:00:36,489 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:36,502 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:36,731 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:36,743 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:36,949 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:36,962 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:37,198 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:37,212 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:37,425 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:37,437 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:37,680 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:37,693 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:37,901 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:37,914 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:38,128 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:38,142 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:38,362 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:38,374 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:38,594 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:38,625 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:38,835 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:38,848 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:39,066 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:39,079 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:39,306 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:39,323 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:39,546 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:39,560 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:39,771 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:39,784 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:39,999 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:40,013 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:40,235 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.234.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:00:40,247 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:00:40,501 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.74 INFO 2025-06-26 13:00:40,685 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.74 INFO 2025-06-26 13:00:40,851 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.74 INFO 2025-06-26 13:00:41,019 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:00:41,197 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 13:00:41,253 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_align.nc INFO 2025-06-26 13:00:41,432 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 13:00:41,436 process.py resample():273 [1] Resampling steps for 2007.234.05 INFO 2025-06-26 13:00:41,437 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:00:41,479 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_align.nc mission netCDF file INFO 2025-06-26 13:00:41,490 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_align.nc mission netCDF file INFO 2025-06-26 13:00:41,492 resample.py get_mission_start_end():1145 [1] navigation: 2007-08-22T21:23:41.156088320 to 2007-08-23T17:22:16.899522304 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:00:41,496 resample.py get_mission_start_end():1145 [1] hs2 : 2007-08-22T21:23:15.657835008 to 2007-08-23T17:22:16.879523840 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 13:00:41,499 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-08-22T21:23:35.316488192 to 2007-08-23T17:22:16.799528960 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 13:00:41,502 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-08-22T21:23:36.006441216 to 2007-08-23T17:22:16.849525760 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 13:00:41,504 resample.py get_mission_start_end():1145 [1] isus : 2007-08-22T21:24:22.203276288 to 2007-08-23T17:22:15.989584640 (0 days 00:00:00.909937664 before mission_end) INFO 2025-06-26 13:00:41,506 resample.py get_mission_start_end():1145 [1] biolume : 2007-08-22T21:23:06.558424064 to 2007-08-23T17:22:15.819561984 (0 days 00:00:01.079960320 before mission_end) INFO 2025-06-26 13:00:41,508 resample.py get_mission_start_end():1145 [1] tailcone : 2007-08-22T21:23:10.868163072 to 2007-08-23T17:22:16.869524480 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 13:00:41,509 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_align.nc mission netCDF file INFO 2025-06-26 13:00:41,509 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,251 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,370 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,491 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,604 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,702 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,799 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,895 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:42,990 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,081 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,170 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,260 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,351 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,440 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,530 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,622 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,710 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,802 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,896 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:43,995 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,088 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,181 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,275 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,312 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,342 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,371 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,406 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,441 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:00:44,934 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_1S.nc INFO 2025-06-26 13:00:49,022 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:01:00,213 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.234.05/dorado_2007.234.05_1S_Gulper.txt INFO 2025-06-26 13:01:00,213 process.py archive():337 [1] Archiving steps for 2007.234.05 INFO 2025-06-26 13:01:00,214 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05, BASE_PATH = /data/auv_data INFO 2025-06-26 13:01:00,215 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:01:00,216 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.234.05_1S.nc INFO 2025-06-26 13:01:00,264 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:01:00,265 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.234.05_cal.nc INFO 2025-06-26 13:01:00,511 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:01:00,513 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.234.05_align.nc INFO 2025-06-26 13:01:00,734 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:01:00,800 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:00,868 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:00,873 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:00,916 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:01,127 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:01,138 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:01,215 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:01,231 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:01,410 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007234/2007.234.05 done. INFO 2025-06-26 13:01:01,410 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:01:01,413 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.234.05_1S_Gulper.txt INFO 2025-06-26 13:01:01,418 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.234.05/dorado_2007.234.05_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 13:01:01,419 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.234.05/dorado_2007.234.05_processing.log /Volumes/AUVCTD/surveys/2007/netcdf