INFO 2025-06-26 13:27:23,127 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 13:27:23,127 process.py process_mission():434 [1] dorado_info[mission]["comment"] = OCCO mission - Northern shelf survey about ESP deployments - got tied up in kelp near Natural Bridges - ctdToUse = ctd1 INFO 2025-06-26 13:27:23,127 process.py process_mission():449 [1] Processing OCCO mission 2007.261.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:27:23,127 process.py download_process():165 [1] Download and processing steps for 2007.261.00 INFO 2025-06-26 13:27:23,127 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007261/2007.261.00 INFO 2025-06-26 13:27:23,127 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007261/2007.261.00 to /data/auv_data/dorado/missionlogs/2007.261.00 INFO 2025-06-26 13:27:29,984 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.261.00 INFO 2025-06-26 13:27:29,985 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/ctdDriver.log (23857019 bytes) INFO 2025-06-26 13:27:31,681 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.261.00/ctdDriver.log: [ 7 30 246 285 331 449 603 832 894 979 1127 1242 1437 1502 1590 1769 1994 2108 2117 2390 2394 2431 2652 2977 3204 3345 3623 3695 3840 4029 4450 4827 5322 5454 6042 7938 8187 10348 10607 10619 10943 11187 11224 12300 13475 13726 13784 15838 16392 16703 16726 17952 18441 24631 25489 27965 28339 30923 31415 33932 38033 38073 41928 43414 46416 47546 47768 50020 52209 52259 53922 64052 65034 68914 71157 77815 78680 80700 82549 91250 91416 91726 94928 95271 97962 102034 104666 104994 105657 106522 107653 109137 111375 112397 118436 123612 128538 130468 131511 132079 137578 138225 142193 142574 143024 143872 144693 145152 151651 151803 152121 158902 159521 162887 165016 170492 173136 173899 177509 180246 182487 182880 183346 191938 196398 198632 198656 208706 211062 212451 215820 218808 221884 225518 231012 233912 242692 243520 244278 245664 251314 251390 252381 254845 258507 259097 262629 263919] INFO 2025-06-26 13:27:31,752 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/ctdDriver2.log (23854901 bytes) INFO 2025-06-26 13:27:33,577 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.261.00/ctdDriver2.log: [ 241 327 598 826 888 1118 1232 1427 1581 1982 2095 2376 2415 2636 2960 3327 3602 3675 4009 4431 4806 4986 5211 5303 5436 5562 6025 8167 10589 10601 10863 10925 11169 12283 13450 13459 13857 15823 16376 16688 16712 16864 18425 21625 23875 24614 25283 27946 28319 28506 30901 31393 33909 38011 38051 41907 43391 47521 47744 48431 52236 64029 65010 71132 78311 78661 80680 82528 83765 91219 91386 91697 94117 94896 97930 102002 102433 104639 104967 105629 106494 107625 109110 111348 112374 116619 118061 123591 124777 125898 128517 128873 130447 131490 132059 132244 137560 142176 142557 143005 143854 144675 145133 151632 151784 152102 158567 158879 162031 162863 164992 165613 170469 173116 173880 177488 180227 182468 182862 191918 196378 198611 198635 201573 205349 208686 212431 214536 215799 216616 218196 218787 225495 242670 244256 245642 251290 251366 252358 252445 258483 259073 262605 263895] INFO 2025-06-26 13:27:33,662 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/gps.log (1375196 bytes) INFO 2025-06-26 13:27:33,812 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/hydroscatlog.log (16284254 bytes) INFO 2025-06-26 13:27:35,720 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.261.00/hydroscatlog.log: [ 16 28 62 68 92 95 289 306 315 355 402 519 597 826 830 885 906 969 1053 1096 1202 1317 1459 1514 1531 1567 1580 1649 1669 1670 1786 1849 2074 2250 2251 2513 2734 3280 3324 3422 3429 3709 3782 3810 4539 4540 4914 4929 5095 5387 5413 5419 5547 5674 6094 6139 6191 6756 7337 7356 7609 8039 8289 9237 9302 10454 10520 10714 10727 10989 11052 11296 11334 11359 11360 11752 11756 12095 13583 13593 13844 13902 13992 15287 15961 16011 16515 16516 16527 16828 16852 17002 17049 17534 18088 20614 20884 21780 22631 22920 23949 25446 25447 28113 28114 28181 28488 28677 28811 29104 30416 30834 30979 31075 31375 31837 34084 34085 37696 38189 38230 38231 38427 38588 39075 42091 43577 44419 45309 45626 46154 46583 46651 47261 47262 47715 47938 47939 48626 50190 51856 52382 52432 52433 54095 57856 59543 60863 61590 62519 63515 64239 64240 64377 64579 65221 65222 66662 66663 67684 67849 67850 69086 69104 70509 71296 71351 71879 72929 76612 78016 78017 78532 78883 80902 82751 83461 84119 84741 88019 88236 91199 91453 91454 91621 91932 92723 95136 98169 98170 99020 99122 101509 102250 103552 104889 104890 105219 105883 106632 106749 106750 107882 111609 111899 112095 112289 112636 112637 116487 118228 118331 118685 118686 122577 123342 123605 123862 123863 125047 130717 131764 132333 132517 135929 135930 136646 137834 142073 142074 142453 142834 144134 144151 144152 144955 145205 145415 152068 152387 155197 158629 159166 159181 163155 163223 165282 165350 165906 166296 166796 167821 168716 168717 170769 172069 172190 173417 174181 177787 178785 180530 181675 182188 182771 183166 183631 185505 187648 189183 192123 192225 193975 194765 196685 198917 198942 201879 202097 203099 205037 205654 207467 208991 211685 212371 212739 216108 218504 219087 219096 222171 223223 224795 225666 225806 226700 231301 232207 232523 234200 237420 239236 241697 242251 242981 243811 244569 247692 251680 252293 252673 252760 255135 255617 255884 256712 258799 259390 261257 262320 264214 265914 266106] INFO 2025-06-26 13:27:35,774 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/navigation.log (79919402 bytes) INFO 2025-06-26 13:27:41,615 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/isuslog.log (1724117 bytes) INFO 2025-06-26 13:27:41,784 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/parosci.log (28526294 bytes) INFO 2025-06-26 13:27:44,271 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/tailCone.log (3241003 bytes) INFO 2025-06-26 13:27:44,669 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.261.00/biolume.log (18471932 bytes) INFO 2025-06-26 13:27:46,517 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:27:47,510 logs2netcdfs.py download_process_logs():807 [1] Time to process: 17.53 seconds WARNING 2025-06-26 13:27:47,510 process.py download_process():196 [1] No lopc.bin file for 2007.261.00 INFO 2025-06-26 13:27:47,510 process.py calibrate():227 [1] Calibration steps for 2007.261.00 INFO 2025-06-26 13:27:47,994 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 13:27:47,996 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:27:48,932 calibrate.py _nudge_pos():1806 [1] 114: 0.200 -0.0000096 -0.0000194 19 0.06 -23.696 -59.797 2007-09-18T20:40:05.647089408 INFO 2025-06-26 13:27:48,983 calibrate.py _nudge_pos():1806 [1] 119: 0.200 0.0004728 -0.0005152 3351 11.33 6.191 -8.429 2007-09-18T20:51:29.650232064 INFO 2025-06-26 13:27:49,741 calibrate.py _nudge_pos():1806 [1] 193: 0.200 0.0000934 -0.0005305 12870 43.17 0.321 -2.277 2007-09-18T21:35:53.647735552 INFO 2025-06-26 13:27:50,559 calibrate.py _nudge_pos():1806 [1] 272: 0.010 0.0001775 -0.0005543 13195 44.10 0.597 -2.329 2007-09-18T22:21:17.851115008 INFO 2025-06-26 13:27:50,631 calibrate.py _nudge_pos():1806 [1] 279: 0.010 0.0000068 -0.0000131 74 0.25 4.108 -9.877 2007-09-18T22:21:38.849676288 INFO 2025-06-26 13:27:51,406 calibrate.py _nudge_pos():1806 [1] 355: 0.020 0.0001481 -0.0004582 12121 40.50 0.543 -2.097 2007-09-18T23:03:23.848072192 INFO 2025-06-26 13:27:52,185 calibrate.py _nudge_pos():1806 [1] 427: 0.020 -0.0000598 -0.0004696 12080 40.33 -0.220 -2.158 2007-09-18T23:44:54.847427072 INFO 2025-06-26 13:27:52,844 calibrate.py _nudge_pos():1806 [1] 491: 0.030 0.0000547 -0.0000030 20 0.06 127.834 -8.854 2007-09-18T23:46:02.852768512 INFO 2025-06-26 13:27:53,244 calibrate.py _nudge_pos():1806 [1] 528: 0.030 0.0002026 -0.0004693 12424 41.50 0.724 -2.095 2007-09-19T00:28:08.849725952 INFO 2025-06-26 13:27:53,387 calibrate.py _nudge_pos():1806 [1] 542: 0.030 0.0000157 0.0000082 30 0.10 24.123 15.647 2007-09-19T00:28:27.848424448 INFO 2025-06-26 13:27:54,242 calibrate.py _nudge_pos():1806 [1] 622: 0.030 0.0000337 -0.0005404 10306 34.40 0.145 -2.911 2007-09-19T01:04:12.851481600 INFO 2025-06-26 13:27:54,274 calibrate.py _nudge_pos():1806 [1] 625: 0.030 0.0000152 -0.0000099 60 0.20 11.462 -9.317 2007-09-19T01:04:26.850522624 INFO 2025-06-26 13:27:54,966 calibrate.py _nudge_pos():1806 [1] 692: 0.040 0.0000763 -0.0000581 2979 9.95 1.138 -1.082 2007-09-19T01:15:29.845104384 INFO 2025-06-26 13:27:55,679 calibrate.py _nudge_pos():1806 [1] 760: 0.040 -0.0002483 -0.0000849 10384 34.68 -1.061 -0.454 2007-09-19T01:51:17.847956224 INFO 2025-06-26 13:27:56,485 calibrate.py _nudge_pos():1806 [1] 837: 0.050 -0.0001570 -0.0000437 6509 21.73 -1.071 -0.373 2007-09-19T02:14:17.843419904 INFO 2025-06-26 13:27:57,235 calibrate.py _nudge_pos():1806 [1] 902: 0.040 0.0000239 0.0000096 15 0.05 75.942 38.125 2007-09-19T02:15:24.848829696 INFO 2025-06-26 13:27:57,289 calibrate.py _nudge_pos():1806 [1] 907: 0.050 -0.0000643 0.0000033 3867 12.91 -0.738 0.047 2007-09-19T02:28:23.845464832 INFO 2025-06-26 13:27:58,113 calibrate.py _nudge_pos():1806 [1] 985: 0.050 0.0000178 0.0003989 13847 46.21 0.057 1.600 2007-09-19T03:15:53.850226176 INFO 2025-06-26 13:27:58,230 calibrate.py _nudge_pos():1806 [1] 996: 0.050 0.0000244 -0.0000184 60 0.20 18.362 -17.337 2007-09-19T03:16:15.848719104 INFO 2025-06-26 13:27:58,812 calibrate.py _nudge_pos():1806 [1] 1050: 0.060 -0.0000404 0.0002879 12447 41.55 -0.144 1.284 2007-09-19T03:58:41.844306432 INFO 2025-06-26 13:27:59,582 calibrate.py _nudge_pos():1806 [1] 1122: 0.060 -0.0000908 0.0002768 13392 44.71 -0.301 1.147 2007-09-19T04:44:35.845644544 INFO 2025-06-26 13:28:00,366 calibrate.py _nudge_pos():1806 [1] 1193: 0.070 -0.0001139 0.0002254 11451 38.23 -0.442 1.093 2007-09-19T05:23:59.843699456 INFO 2025-06-26 13:28:01,148 calibrate.py _nudge_pos():1806 [1] 1265: 0.070 -0.0001232 0.0003192 12590 42.01 -0.435 1.408 2007-09-19T06:07:11.846135040 INFO 2025-06-26 13:28:01,920 calibrate.py _nudge_pos():1806 [1] 1336: 0.070 -0.0000246 0.0001427 3845 12.83 -0.284 2.061 2007-09-19T06:21:11.848591104 INFO 2025-06-26 13:28:02,664 calibrate.py _nudge_pos():1806 [1] 1395: 0.070 0.0001145 0.0000372 11931 39.83 0.426 0.173 2007-09-19T07:01:59.850891264 INFO 2025-06-26 13:28:02,777 calibrate.py _nudge_pos():1806 [1] 1405: 0.070 -0.0000112 -0.0000082 85 0.28 -5.920 -5.421 2007-09-19T07:02:25.849110272 INFO 2025-06-26 13:28:03,394 calibrate.py _nudge_pos():1806 [1] 1462: 0.080 0.0000438 -0.0000030 5794 19.33 0.336 -0.029 2007-09-19T07:22:41.845808896 INFO 2025-06-26 13:28:04,178 calibrate.py _nudge_pos():1806 [1] 1533: 0.090 0.0000443 -0.0000082 3488 11.63 0.564 -0.131 2007-09-19T07:35:29.843197696 INFO 2025-06-26 13:28:04,880 calibrate.py _nudge_pos():1806 [1] 1597: 0.080 0.0001661 -0.0003938 12231 40.85 0.602 -1.786 2007-09-19T08:17:23.850976256 INFO 2025-06-26 13:28:05,696 calibrate.py _nudge_pos():1806 [1] 1670: 0.090 0.0001110 -0.0002268 7129 23.80 0.691 -1.766 2007-09-19T08:42:23.848219392 INFO 2025-06-26 13:28:06,519 calibrate.py _nudge_pos():1806 [1] 1743: 0.100 0.0000397 -0.0002278 7254 24.20 0.243 -1.744 2007-09-19T09:07:47.843818496 INFO 2025-06-26 13:28:07,411 calibrate.py _nudge_pos():1806 [1] 1822: 0.090 0.0000715 -0.0003188 9890 33.03 0.321 -1.788 2007-09-19T09:42:11.852424192 INFO 2025-06-26 13:28:08,275 calibrate.py _nudge_pos():1806 [1] 1899: 0.100 0.0002181 -0.0003634 13448 44.90 0.719 -1.500 2007-09-19T10:28:21.852666112 INFO 2025-06-26 13:28:09,070 calibrate.py _nudge_pos():1806 [1] 1971: 0.100 0.0001146 -0.0000489 4452 14.85 1.143 -0.610 2007-09-19T10:44:23.846765056 INFO 2025-06-26 13:31:27,288 calibrate.py _nudge_pos():1862 [1] 19055: - - - 3 0.01 - - INFO 2025-06-26 13:31:27,289 calibrate.py _nudge_pos():1868 [1] Points in final series = 338485 WARNING 2025-06-26 13:31:27,913 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 13:32:03,187 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 313 of 271065 INFO 2025-06-26 13:32:05,362 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:32:24,571 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:32:26,608 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:32:26,612 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.261.00/ctd1.nc INFO 2025-06-26 13:32:26,614 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 13:32:26,614 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 13:32:26,615 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:32:41,477 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:32:43,463 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:32:43,467 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.261.00/ctd2.nc INFO 2025-06-26 13:32:43,469 calibrate.py _range_qc_combined_nc():898 [1] Setting 166 ctd2_salinity values to NaN INFO 2025-06-26 13:32:43,469 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 13:32:43,469 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:32:43,568 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:32:46,710 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4069083 4069084 4069085] INFO 2025-06-26 13:32:47,409 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:32:47,416 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 13:32:47,416 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.261.00 ERROR 2025-06-26 13:32:47,417 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.261.00 INFO 2025-06-26 13:32:47,541 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_cal.nc INFO 2025-06-26 13:33:08,650 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 13:33:08,656 process.py align():251 [1] Alignment steps for 2007.261.00 INFO 2025-06-26 13:33:08,699 align.py process_cal():139 [1] Processing dorado_2007.261.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.261.00 INFO 2025-06-26 13:33:08,791 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:33:08,801 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:33:09,014 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:33:09,026 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:33:09,244 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:33:09,255 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:33:09,384 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:33:09,385 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:33:09,467 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:33:09,479 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:33:09,692 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:09,703 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:09,884 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:09,895 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:10,082 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:10,093 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:10,294 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:10,304 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:10,495 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:10,505 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:10,691 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:10,701 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:10,884 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:10,895 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:11,093 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:11,103 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:11,305 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:11,316 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:11,497 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:11,507 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:11,692 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:11,703 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:11,884 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:11,895 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:12,079 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:12,089 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:12,269 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:12,280 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:12,463 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:12,473 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:12,664 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:12,676 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:12,859 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:12,869 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:13,051 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:13,061 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:13,246 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:13,257 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:13,440 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.261.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:33:13,450 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:33:13,674 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 13:33:13,810 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 13:33:13,950 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.79 INFO 2025-06-26 13:33:14,095 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:33:14,244 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 13:33:14,311 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_align.nc INFO 2025-06-26 13:33:14,466 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 13:33:14,468 process.py resample():273 [1] Resampling steps for 2007.261.00 INFO 2025-06-26 13:33:14,469 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:33:14,502 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_align.nc mission netCDF file INFO 2025-06-26 13:33:14,510 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_align.nc mission netCDF file INFO 2025-06-26 13:33:14,512 resample.py get_mission_start_end():1145 [1] navigation: 2007-09-18T20:38:42.062815488 to 2007-09-19T15:29:40.444197888 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:33:14,515 resample.py get_mission_start_end():1145 [1] hs2 : 2007-09-18T20:38:19.734344960 to 2007-09-19T15:29:40.344204544 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 13:33:14,518 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-09-18T20:38:35.043296256 to 2007-09-19T15:29:40.354203904 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 13:33:14,520 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-09-18T20:38:35.633255680 to 2007-09-19T15:29:40.424199168 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 13:33:14,522 resample.py get_mission_start_end():1145 [1] isus : 2007-09-18T20:39:27.149726720 to 2007-09-19T15:29:40.214213632 (0 days 00:00:00.229984256 before mission_end) INFO 2025-06-26 13:33:14,524 resample.py get_mission_start_end():1145 [1] biolume : 2007-09-18T20:38:08.555076608 to 2007-09-19T15:29:39.254245120 (0 days 00:00:01.189952768 before mission_end) INFO 2025-06-26 13:33:14,525 resample.py get_mission_start_end():1145 [1] tailcone : 2007-09-18T20:38:13.024804608 to 2007-09-19T15:29:39.694249216 (0 days 00:00:00.749948672 before mission_end) INFO 2025-06-26 13:33:14,526 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_align.nc mission netCDF file INFO 2025-06-26 13:33:14,526 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,211 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,321 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,428 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,535 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,627 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,724 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,813 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,901 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:15,987 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,071 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,155 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,242 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,326 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,411 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,494 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,578 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,666 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,764 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,859 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:16,948 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,037 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,125 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,159 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,189 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,217 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,249 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,282 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:33:17,765 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_1S.nc INFO 2025-06-26 13:33:21,030 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:33:30,693 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.261.00/dorado_2007.261.00_1S_Gulper.txt INFO 2025-06-26 13:33:30,694 process.py archive():337 [1] Archiving steps for 2007.261.00 INFO 2025-06-26 13:33:30,694 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00, BASE_PATH = /data/auv_data INFO 2025-06-26 13:33:30,696 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:33:30,696 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.261.00_1S.nc INFO 2025-06-26 13:33:30,746 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:33:30,747 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.261.00_cal.nc INFO 2025-06-26 13:33:30,996 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:33:30,998 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.261.00_align.nc INFO 2025-06-26 13:33:31,222 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:33:31,290 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,357 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,366 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,417 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,617 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,627 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,705 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,721 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,901 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007261/2007.261.00 done. INFO 2025-06-26 13:33:31,901 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:33:31,903 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.261.00_1S_Gulper.txt INFO 2025-06-26 13:33:31,907 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.261.00/dorado_2007.261.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 13:33:31,908 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.261.00/dorado_2007.261.00_processing.log /Volumes/AUVCTD/surveys/2007/netcdf