INFO 2025-06-26 13:47:44,044 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 13:47:44,044 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Canyon Axis with Gulper - ctdToUse = ctd1 INFO 2025-06-26 13:47:44,044 process.py process_mission():449 [1] Processing AUVCTD mission 2007.331.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:47:44,044 process.py download_process():165 [1] Download and processing steps for 2007.331.01 INFO 2025-06-26 13:47:44,044 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007331/2007.331.01 INFO 2025-06-26 13:47:44,045 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007331/2007.331.01 to /data/auv_data/dorado/missionlogs/2007.331.01 INFO 2025-06-26 13:47:50,705 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.331.01 INFO 2025-06-26 13:47:50,705 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/ctdDriver.log (23857548 bytes) INFO 2025-06-26 13:47:52,398 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.331.01/ctdDriver.log: [ 367 542 720 729 808 975 976 1097 1182 1311 1467 1531 1624 1726 1820 2214 2268 2710 2768 3126 3332 3620 3649 3663 4755 4998 5338 5466 6528 7200 7771 8030 8408 8503 9582 11517 14219 14382 16885 18461 19792 21103 21197 21245 24255 25343 25589 31638 31812 33095 34046 40604 44032 44134 45244 45599 45789 49899 51767 51960 52615 57012 59824 63116 71428 74046 80843 81162 85531 92594 98330 102499 104678 105676 107855 108765 109608 112386 114923 115461 116474 119100 123292 128504 132526 137290 138376 139239 141836 143795 145166 152270 159377 168544 168754 172782 174757 175600 175661 179495 184357 194836 197995 199191 199637 202040 206350 216263 220593 223824 230486 230789 246639 251492 255998 259615 260151 265602] INFO 2025-06-26 13:47:52,466 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/ctdDriver2.log (23858685 bytes) INFO 2025-06-26 13:47:54,144 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.331.01/ctdDriver2.log: [ 14 388 456 563 741 1114 1199 1328 1547 1640 1685 1743 1767 1837 2230 2283 2727 2785 3638 3667 3681 4773 7215 7785 8044 8422 8517 9596 9976 11531 12067 14234 14397 16977 17147 18472 21113 24263 25428 25592 31639 31813 33096 34048 40200 40605 44134 45244 45599 45789 49225 49899 51960 52615 60417 63114 71424 74042 74500 78816 81159 85528 92592 102498 103077 105674 107857 109610 111839 112388 114925 116474 119101 123294 132526 138377 139241 141841 143799 145170 145999 148191 151902 159383 167220 168552 168761 169838 172796 173607 174771 175614 179508 184373 191732 193669 194850 198006 199648 205602 206359 216273 217504 220603 228815 230802 235608 241338 246651 251504 256010 259627 261563 265166] INFO 2025-06-26 13:47:54,221 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/gps.log (120380 bytes) INFO 2025-06-26 13:47:54,243 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/hydroscatlog.log (16292414 bytes) INFO 2025-06-26 13:47:56,178 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.331.01/hydroscatlog.log: [ 3 4 5 6 7 8 9 10 37 38 77 100 102 108 122 240 241 328 486 533 534 557 558 666 734 750 786 826 849 858 937 938 1096 1131 1132 1208 1230 1267 1316 1542 1645 1658 1764 1810 1868 1893 1964 2410 2413 2414 2512 2513 2583 2584 2827 2835 2864 2922 2923 3280 3487 3556 3584 3670 3697 3780 3810 3825 3826 4347 4521 4919 5024 5163 5164 5256 5263 5370 5371 5507 5543 5636 5637 5764 6367 6388 6513 6551 7376 7544 7655 7677 7813 7951 8209 8589 8685 8686 9546 9768 9777 10148 10805 11085 11322 11450 11628 11711 11712 12246 12460 13063 13160 13850 14140 14313 14419 14420 14425 14680 15232 16994 17093 17175 17346 18282 18587 18674 19643 20005 21316 21410 21787 22004 22452 22742 23738 24473 24474 25481 25564 25813 25814 28010 28011 29496 29957 30271 31597 31870 32045 32772 32773 33328 33566 34017 34384 35380 37087 38248 38725 38772 40396 40846 41844 44275 44377 44378 45488 45658 45845 49471 50147 50922 52208 52866 52965 55485 57267 57268 58927 60080 60675 61341 62258 63374 65645 67195 68741 70870 71690 72359 72473 74310 74754 74769 77593 78387 79088 79329 81116 81437 85670 85807 85897 88263 88552 88553 91050 91051 92424 92525 92873 93400 93401 98385 98610 99242 100900 102781 102782 103134 103362 104961 105920 105961 108146 108406 109058 109902 112130 112131 112365 112680 112681 113364 114282 114283 115220 115221 115760 115922 116776 117024 119404 122468 123422 123597 123598 126118 128809 129364 130924 131253 131356 132304 132838 136743 136792 137605 138371 138694 139559 142157 142158 144116 145488 146275 146322 146382 147555 148526 149234 149235 152608 152996 153457 154357 159727 160960 164588 166428 166840 167569 168458 168901 169111 169112 170189 172168 173692 173963 174810 174811 175129 175972 175973 179872 181080 182846 184187 184188 184745 185024 186593 187644 188201 190977 192107 193310 195231 195320 195321 196100 198390 198488 199588 200036 200384 202437 205430 205990 206142 206750 212040 212042 213462 213491 215614 216663 217555 217896 219140 220178 220995 220996 222962 223047 223780 224230 225804 226898 228500 229210 230895 231198 231199 231981 233617 236004 236007 238011 238012 238065 238809 240334 241735 241736 243507 245125 246210 246848 247052 250030 250031 251012 251906 251907 252240 252242 254092 254093 256414 259358 260030 260031 261969 262651 265572 265573 266023 266625 267204 267205 267987] INFO 2025-06-26 13:47:56,231 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/navigation.log (79928606 bytes) INFO 2025-06-26 13:48:01,948 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/isuslog.log (1689461 bytes) INFO 2025-06-26 13:48:02,114 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.331.01/isuslog.log: [1 2 3 4 5 6 7 8 9] INFO 2025-06-26 13:48:02,120 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/parosci.log (28534214 bytes) INFO 2025-06-26 13:48:04,513 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/tailCone.log (3286123 bytes) INFO 2025-06-26 13:48:04,924 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.331.01/biolume.log (18480908 bytes) INFO 2025-06-26 13:48:06,660 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:48:07,621 logs2netcdfs.py download_process_logs():807 [1] Time to process: 16.92 seconds WARNING 2025-06-26 13:48:07,622 process.py download_process():196 [1] No lopc.bin file for 2007.331.01 INFO 2025-06-26 13:48:07,622 process.py calibrate():227 [1] Calibration steps for 2007.331.01 INFO 2025-06-26 13:48:08,095 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 13:48:08,098 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:48:08,933 calibrate.py _nudge_pos():1806 [1] 104: 0.010 -0.0002950 -0.0002851 3155 10.80 -4.057 -4.892 2007-11-27T23:15:59.534863872 INFO 2025-06-26 13:48:09,727 calibrate.py _nudge_pos():1806 [1] 181: 0.010 -0.0024857 -0.0013033 16033 53.83 -6.856 -4.486 2007-11-28T00:11:05.538386944 INFO 2025-06-26 13:48:10,393 calibrate.py _nudge_pos():1806 [1] 246: 0.010 -0.0068779 0.0014610 9754 32.63 -31.299 8.297 2007-11-28T00:44:47.539870464 INFO 2025-06-26 13:48:11,068 calibrate.py _nudge_pos():1806 [1] 312: 0.010 -0.0086963 0.0023349 15046 50.30 -25.675 8.602 2007-11-28T01:36:11.538602240 INFO 2025-06-26 13:48:11,541 calibrate.py _nudge_pos():1806 [1] 358: 0.020 0.0000396 0.0000020 25 0.08 73.600 4.528 2007-11-28T01:37:01.535177216 INFO 2025-06-26 13:48:11,563 calibrate.py _nudge_pos():1806 [1] 360: 0.020 -0.0000636 0.0000244 55 0.18 -52.476 25.168 2007-11-28T01:37:13.534355200 INFO 2025-06-26 13:48:11,607 calibrate.py _nudge_pos():1806 [1] 364: 0.020 -0.0021222 0.0028228 7671 25.61 -12.305 20.422 2007-11-28T02:02:53.538857728 INFO 2025-06-26 13:48:11,731 calibrate.py _nudge_pos():1806 [1] 376: 0.020 -0.0000397 0.0000182 25 0.08 -73.777 42.170 2007-11-28T02:03:09.537761792 INFO 2025-06-26 13:48:12,283 calibrate.py _nudge_pos():1806 [1] 429: 0.020 0.0000830 0.0011486 13366 44.65 0.276 4.767 2007-11-28T02:48:41.540606464 INFO 2025-06-26 13:48:12,999 calibrate.py _nudge_pos():1806 [1] 498: 0.030 -0.0000170 0.0000165 15 0.05 -54.190 65.586 2007-11-28T02:49:54.535606272 INFO 2025-06-26 13:48:13,023 calibrate.py _nudge_pos():1806 [1] 500: 0.020 -0.0105475 0.0034567 17907 59.76 -26.213 10.718 2007-11-28T03:49:41.539879680 INFO 2025-06-26 13:48:13,507 calibrate.py _nudge_pos():1806 [1] 546: 0.030 0.0004100 -0.0093597 14593 48.75 1.249 -35.579 2007-11-28T04:39:11.536420864 INFO 2025-06-26 13:48:13,668 calibrate.py _nudge_pos():1806 [1] 561: 0.030 0.0004053 -0.0094886 30 0.10 622.960 -18189.858 2007-11-28T04:39:31.535050752 INFO 2025-06-26 13:48:15,047 calibrate.py _nudge_pos():1806 [1] 692: 0.020 0.0048662 -0.0106580 14970 49.98 14.467 -39.514 2007-11-28T05:31:41.540630784 INFO 2025-06-26 13:48:15,534 calibrate.py _nudge_pos():1806 [1] 738: 0.030 -0.0000579 0.0000595 15 0.05 -184.482 236.107 2007-11-28T05:32:29.537342720 INFO 2025-06-26 13:48:15,567 calibrate.py _nudge_pos():1806 [1] 741: 0.030 -0.0096736 0.0052266 17483 58.36 -24.626 16.594 2007-11-28T06:30:53.537302272 INFO 2025-06-26 13:48:16,224 calibrate.py _nudge_pos():1806 [1] 801: 0.020 0.0000041 -0.0000256 15 0.05 13.178 -101.624 2007-11-28T06:31:55.543054592 INFO 2025-06-26 13:48:16,331 calibrate.py _nudge_pos():1806 [1] 811: 0.030 -0.0032505 -0.0086058 10690 35.71 -13.525 -44.652 2007-11-28T07:07:47.535633152 INFO 2025-06-26 13:48:16,492 calibrate.py _nudge_pos():1806 [1] 826: 0.030 -0.0000055 0.0000042 20 0.06 -12.907 12.283 2007-11-28T07:08:05.534400000 INFO 2025-06-26 13:48:17,084 calibrate.py _nudge_pos():1806 [1] 881: 0.030 0.0088570 -0.0047885 18489 61.70 21.331 -14.382 2007-11-28T08:10:41.537096192 INFO 2025-06-26 13:48:17,703 calibrate.py _nudge_pos():1806 [1] 938: 0.040 0.0057755 -0.0027845 18350 61.26 14.007 -8.422 2007-11-28T09:12:53.541436416 INFO 2025-06-26 13:48:18,586 calibrate.py _nudge_pos():1806 [1] 1020: 0.040 0.0015985 0.0000915 18376 61.35 3.871 0.277 2007-11-28T10:15:35.543721728 INFO 2025-06-26 13:48:19,266 calibrate.py _nudge_pos():1806 [1] 1082: 0.040 -0.0010229 0.0020826 18440 61.58 -2.467 6.267 2007-11-28T11:18:11.536418560 INFO 2025-06-26 13:48:19,907 calibrate.py _nudge_pos():1806 [1] 1141: 0.040 -0.0010729 0.0015186 9775 32.63 -4.884 8.624 2007-11-28T11:51:47.538312960 INFO 2025-06-26 13:48:20,543 calibrate.py _nudge_pos():1806 [1] 1198: 0.040 -0.0022302 0.0038475 17090 57.06 -5.804 12.494 2007-11-28T12:49:47.539916544 INFO 2025-06-26 13:48:21,243 calibrate.py _nudge_pos():1806 [1] 1261: 0.050 0.0000077 0.0000425 25 0.08 14.205 98.364 2007-11-28T12:50:54.535326976 INFO 2025-06-26 13:48:21,277 calibrate.py _nudge_pos():1806 [1] 1264: 0.040 -0.0012887 0.0037654 12600 42.05 -4.551 16.594 2007-11-28T13:32:59.542352128 INFO 2025-06-26 13:48:21,975 calibrate.py _nudge_pos():1806 [1] 1322: 0.060 0.0008554 0.0039256 18470 61.65 2.060 11.800 2007-11-28T14:35:35.535048960 INFO 2025-06-26 13:48:22,478 calibrate.py _nudge_pos():1806 [1] 1367: 0.060 0.0006683 0.0011764 9304 31.06 3.194 7.017 2007-11-28T15:07:23.534342144 INFO 2025-06-26 13:48:23,174 calibrate.py _nudge_pos():1806 [1] 1430: 0.060 0.0023176 0.0006732 18539 61.88 5.560 2.016 2007-11-28T16:10:19.535668224 INFO 2025-06-26 13:48:23,752 calibrate.py _nudge_pos():1806 [1] 1482: 0.050 0.0008008 0.0008140 9530 31.81 3.736 4.741 2007-11-28T16:42:59.541398784 INFO 2025-06-26 13:48:24,416 calibrate.py _nudge_pos():1806 [1] 1541: 0.060 0.0016471 0.0011841 14961 49.93 4.896 4.394 2007-11-28T17:33:53.542185216 INFO 2025-06-26 13:48:25,400 calibrate.py _nudge_pos():1806 [1] 1628: 0.060 0.0004347 0.0002724 5898 19.66 3.281 2.567 2007-11-28T17:54:59.535458816 INFO 2025-06-26 13:48:25,756 calibrate.py _nudge_pos():1862 [1] 1627: - - - 4 0.01 - - INFO 2025-06-26 13:48:25,756 calibrate.py _nudge_pos():1868 [1] Points in final series = 338544 WARNING 2025-06-26 13:48:26,209 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 13:49:02,485 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:49:21,873 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 32 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:49:23,921 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 32 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:49:23,925 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.331.01/ctd1.nc INFO 2025-06-26 13:49:23,927 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:49:23,927 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 13:49:23,927 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:49:38,868 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:49:40,925 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:49:40,929 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.331.01/ctd2.nc INFO 2025-06-26 13:49:40,930 calibrate.py _range_qc_combined_nc():898 [1] Setting 119 ctd2_salinity values to NaN INFO 2025-06-26 13:49:40,931 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 13:49:40,931 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:49:43,428 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:49:46,547 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4022964 4022965 4022966] INFO 2025-06-26 13:49:47,223 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -7 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 13:49:47,230 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 13:49:47,230 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.331.01 ERROR 2025-06-26 13:49:47,230 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.331.01 INFO 2025-06-26 13:49:47,287 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_cal.nc INFO 2025-06-26 13:50:08,238 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 13:50:08,244 process.py align():251 [1] Alignment steps for 2007.331.01 INFO 2025-06-26 13:50:08,286 align.py process_cal():139 [1] Processing dorado_2007.331.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.331.01 INFO 2025-06-26 13:50:08,373 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:50:08,382 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:50:08,606 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:50:08,619 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:50:08,828 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:50:08,840 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:50:08,969 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:50:08,969 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:50:09,054 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:50:09,065 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:50:09,270 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:09,281 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:09,463 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:09,472 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:09,654 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:09,664 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:09,842 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:09,851 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:10,037 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:10,048 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:10,227 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:10,237 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:10,417 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:10,427 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:10,607 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:10,616 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:10,796 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:10,806 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:10,986 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:10,998 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:11,179 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:11,189 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:11,371 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:11,381 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:11,563 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:11,572 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:11,752 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:11,762 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:11,940 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:11,950 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:12,138 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:12,151 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:12,332 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:12,342 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:12,524 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:12,534 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:12,715 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:12,725 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:12,904 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.331.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:50:12,914 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:50:13,130 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:50:13,265 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:50:13,403 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:50:13,548 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:50:13,692 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 13:50:13,733 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_align.nc INFO 2025-06-26 13:50:13,880 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 13:50:13,882 process.py resample():273 [1] Resampling steps for 2007.331.01 INFO 2025-06-26 13:50:13,883 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:50:13,916 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_align.nc mission netCDF file INFO 2025-06-26 13:50:13,924 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_align.nc mission netCDF file INFO 2025-06-26 13:50:13,926 resample.py get_mission_start_end():1145 [1] navigation: 2007-11-27T23:04:02.323996416 to 2007-11-28T17:55:31.383277056 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 13:50:13,929 resample.py get_mission_start_end():1145 [1] hs2 : 2007-11-27T23:03:37.335707904 to 2007-11-28T17:55:31.403275776 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:50:13,931 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-11-27T23:04:05.863753728 to 2007-11-28T17:55:31.393276416 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 13:50:13,934 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-11-27T23:03:59.624181248 to 2007-11-28T17:55:31.333280512 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 13:50:13,936 resample.py get_mission_start_end():1145 [1] isus : 2007-11-27T23:04:28.682190592 to 2007-11-28T17:55:30.983304448 (0 days 00:00:00.419971328 before mission_end) INFO 2025-06-26 13:50:13,937 resample.py get_mission_start_end():1145 [1] biolume : 2007-11-27T23:03:25.956453376 to 2007-11-28T17:55:30.943272960 (0 days 00:00:00.460002816 before mission_end) INFO 2025-06-26 13:50:13,939 resample.py get_mission_start_end():1145 [1] tailcone : 2007-11-27T23:03:35.915805440 to 2007-11-28T17:55:31.043300352 (0 days 00:00:00.359975424 before mission_end) INFO 2025-06-26 13:50:13,939 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_align.nc mission netCDF file INFO 2025-06-26 13:50:13,940 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:14,629 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:14,739 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:14,846 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:14,954 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,047 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,143 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,233 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,322 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,407 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,491 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,577 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,662 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,746 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,829 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,912 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:15,995 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,083 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,175 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,270 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,359 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,448 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,538 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,573 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,602 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,630 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,663 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:16,696 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:50:17,178 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_1S.nc INFO 2025-06-26 13:50:20,080 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:50:30,857 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.331.01/dorado_2007.331.01_1S_Gulper.txt INFO 2025-06-26 13:50:30,857 process.py archive():337 [1] Archiving steps for 2007.331.01 INFO 2025-06-26 13:50:30,857 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01, BASE_PATH = /data/auv_data INFO 2025-06-26 13:50:30,858 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:50:30,859 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.331.01_1S.nc INFO 2025-06-26 13:50:30,905 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:50:30,906 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.331.01_cal.nc INFO 2025-06-26 13:50:31,153 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:50:31,155 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.331.01_align.nc INFO 2025-06-26 13:50:31,387 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:50:31,455 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:31,518 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:31,523 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:31,568 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:31,787 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:31,798 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:31,884 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:31,900 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:32,072 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007331/2007.331.01 done. INFO 2025-06-26 13:50:32,073 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:50:32,074 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.331.01_1S_Gulper.txt INFO 2025-06-26 13:50:32,079 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.331.01/dorado_2007.331.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 13:50:32,079 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.331.01/dorado_2007.331.01_processing.log /Volumes/AUVCTD/surveys/2007/netcdf