INFO 2025-06-26 12:08:21,999 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 12:08:21,999 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Standard Biolume run. CTD1 was noisey - ctdToUse = ctd1 INFO 2025-06-26 12:08:21,999 process.py process_mission():449 [1] Processing BIOLUME mission 2006.291.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:08:21,999 process.py download_process():165 [1] Download and processing steps for 2006.291.03 INFO 2025-06-26 12:08:21,999 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006291/2006.291.03 INFO 2025-06-26 12:08:21,999 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006291/2006.291.03 to /data/auv_data/dorado/missionlogs/2006.291.03 INFO 2025-06-26 12:08:27,863 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.291.03 INFO 2025-06-26 12:08:27,863 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/ctdDriver.log (16320787 bytes) INFO 2025-06-26 12:08:29,016 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.291.03/ctdDriver.log: [ 59 200 434 664 1508 1591 1620 1765 3344 5283 6241 9620 11269 12074 13493 20905 22152 22569 24915 27075 28258 31349 34569 36300 43841 49292 49571 50541 54750 60245 78071 78556 82339 94537 100129 107762 117034 147014 152648 154516 159661 165688] INFO 2025-06-26 12:08:29,065 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/ctdDriver2.log (16320957 bytes) INFO 2025-06-26 12:08:30,248 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.291.03/ctdDriver2.log: [ 61 202 666 1021 3266 4386 11046 11151 15776 20712 24912 27073 34576 36309 40628 43852 49583 61234 62565 62748 79552 94408 105844 107773 117043 126221 151435 166417 167200 169669 174730 179624] INFO 2025-06-26 12:08:30,308 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/gps.log (79700 bytes) INFO 2025-06-26 12:08:30,325 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/hydroscatlog.log (11135354 bytes) INFO 2025-06-26 12:08:31,667 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.291.03/hydroscatlog.log: [ 4 10 44 287 360 450 649 720 810 940 1096 1099 1100 1374 1578 2993 3402 4128 4989 5065 5172 5434 5629 6452 7410 7483 7712 9685 11213 11219 12055 12141 14579 15118 15649 24321 28338 30371 30618 31433 34660 35992 41742 42107 43934 45545 59875 66989 73842 73975 77302 78586 81209 82451 87151 88317 99144 102149 102539 107876 109502 109976 112230 117149 124645 125977 126327 129909 130982 138090 142341 159420 159788 161112 165813 166530 167313 173638 174839 177292 178901 181004 183724 183760] INFO 2025-06-26 12:08:31,703 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/navigation.log (54696194 bytes) INFO 2025-06-26 12:08:35,658 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/isuslog.log (1115285 bytes) INFO 2025-06-26 12:08:35,768 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/parosci.log (23814950 bytes) INFO 2025-06-26 12:08:37,721 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.291.03/parosci.log: [ 1 2 6 7 16 17 18 19 27 28 57 73 257 258 656 657 658 731 732 796 797 798 999 1381 1382 1383 1765 1766 1767 2196 2469 2470 2540 3678 3963 4146 4197 4219 4353 4354 4417 4418 4492 4493 5412 5925 5927 5965 5966 5967 6587 7995 7996 8880 8892 8893 10299 10300 10301 10302 11026 13185 13186 13328 13329 13330 13335 13336 13814 13816 15032 15074 15076 15405 15406 15408 16838 16839 16924 17232 17662 17663 19984 19985 19986 19987 20205 20207 23063 23064 23065 25674 25870 25871 25912 25913 25915 26356 27629 28174 28175 29687 29688 29969 29970 30225 30226 30275 30276 30751 30752 32203 32205 32206 32434 32435 34528 34529 35349 35351 38948 39374 41809 41810 44514 44516 45252 45254 45985 45986 52510 52511 56050 56051 56052 59398 61785 61786 64223 64224 65005 65007 73458 73459 74277 74279 75664 75666 75667 75752 75753 75754 81190 81849 81850 84060 87864 87865 95650 95652 97296 100209 100210 100211 101581 109841 110242 110243 112583 112743 112744 117467 117468 117469 119355 119357 122078 132056 132802 141093 144251 144252 160115 160116 161371 162873 163986 163987 163988 165346 167548 167549 172645 172921 185773 185774 192970 192972 193505 193506 197477 197478 197479 197836 198171 216300 216301 220510 233089 234569 234570 234623 236212 236213 236214 236417 236418 244712 244713 244714 250427 258961 273194 274235 274236 282805 282806 287195 292851 292853 292854 294118 294119 296118 307718 307719 308335 308336 312251 312252 312901 312902 322024 327355 327356 333326 333327 335170 335171 337808 337809 337810 347381 347382 356565 356567 373397 381499 381501 386175 386176 387213 388247 407128 407129 408490 409136 409829 413477 420261 425189 425190 426240 426241 427513 427514 427515 453548 453550 453925 453926 464241 468880 468882 468883 469774 469776 474000 474001 480342 483250 483928 490788 493630 493632 493633] INFO 2025-06-26 12:08:37,790 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/tailCone.log (11117851 bytes) INFO 2025-06-26 12:08:39,172 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.291.03/biolume.log (12630460 bytes) INFO 2025-06-26 12:08:40,382 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:08:41,040 logs2netcdfs.py download_process_logs():807 [1] Time to process: 13.18 seconds WARNING 2025-06-26 12:08:41,040 process.py download_process():196 [1] No lopc.bin file for 2006.291.03 INFO 2025-06-26 12:08:41,040 process.py calibrate():227 [1] Calibration steps for 2006.291.03 INFO 2025-06-26 12:08:41,463 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 12:08:41,465 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:08:42,196 calibrate.py _nudge_pos():1806 [1] 92: 0.050 -0.0008559 -0.0004700 2529 8.55 -14.892 -10.190 2006-10-18T01:32:18.135281920 INFO 2025-06-26 12:08:42,802 calibrate.py _nudge_pos():1806 [1] 153: 0.040 -0.0025838 -0.0020521 7050 23.60 -16.281 -16.115 2006-10-18T01:56:54.144168192 INFO 2025-06-26 12:08:43,095 calibrate.py _nudge_pos():1806 [1] 182: 0.050 -0.0047941 -0.0034349 10910 36.43 -19.562 -17.471 2006-10-18T02:33:48.142499072 INFO 2025-06-26 12:08:43,750 calibrate.py _nudge_pos():1806 [1] 247: 0.060 -0.0056368 -0.0035944 11484 38.30 -21.873 -17.392 2006-10-18T03:13:12.140553984 INFO 2025-06-26 12:08:43,771 calibrate.py _nudge_pos():1806 [1] 249: 0.060 0.0000381 -0.0000320 35 0.11 49.977 -52.377 2006-10-18T03:13:20.140006144 INFO 2025-06-26 12:08:43,901 calibrate.py _nudge_pos():1806 [1] 262: 0.050 0.0000302 -0.0000491 35 0.11 39.650 -80.296 2006-10-18T03:13:39.138704640 INFO 2025-06-26 12:08:44,157 calibrate.py _nudge_pos():1806 [1] 287: 0.060 -0.0063180 -0.0038806 12334 41.15 -22.810 -17.476 2006-10-18T03:55:12.137922304 INFO 2025-06-26 12:08:44,544 calibrate.py _nudge_pos():1806 [1] 325: 0.060 -0.0084180 -0.0029826 11686 38.98 -32.072 -14.178 2006-10-18T04:34:48.145154816 INFO 2025-06-26 12:08:44,854 calibrate.py _nudge_pos():1806 [1] 356: 0.070 -0.0000220 0.0000050 15 0.05 -69.905 19.967 2006-10-18T04:35:21.142894336 INFO 2025-06-26 12:08:44,884 calibrate.py _nudge_pos():1806 [1] 359: 0.080 -0.0052773 -0.0011847 7083 23.61 -33.183 -9.297 2006-10-18T04:59:00.135686400 INFO 2025-06-26 12:08:45,249 calibrate.py _nudge_pos():1806 [1] 394: 0.080 -0.0022479 -0.0003769 4027 13.43 -24.850 -5.200 2006-10-18T05:13:00.138142464 INFO 2025-06-26 12:08:45,625 calibrate.py _nudge_pos():1806 [1] 431: 0.080 -0.0030877 0.0020205 9292 31.00 -14.785 12.078 2006-10-18T05:44:36.138257408 INFO 2025-06-26 12:08:46,096 calibrate.py _nudge_pos():1806 [1] 477: 0.090 -0.0023627 0.0018810 9339 31.15 -11.256 11.190 2006-10-18T06:16:30.137139456 INFO 2025-06-26 12:08:46,472 calibrate.py _nudge_pos():1806 [1] 514: 0.090 -0.0024535 0.0018798 11721 39.10 -9.308 8.909 2006-10-18T06:56:12.143960832 INFO 2025-06-26 12:08:46,914 calibrate.py _nudge_pos():1806 [1] 557: 0.080 -0.0021098 0.0016349 11421 38.10 -8.212 7.952 2006-10-18T07:35:00.144481792 INFO 2025-06-26 12:08:47,348 calibrate.py _nudge_pos():1806 [1] 599: 0.100 -0.0050505 0.0022255 11758 39.21 -19.090 10.517 2006-10-18T08:14:54.140482048 INFO 2025-06-26 12:08:47,811 calibrate.py _nudge_pos():1806 [1] 643: 0.110 -0.0046983 0.0023810 11298 37.68 -18.475 11.709 2006-10-18T08:53:18.142647040 INFO 2025-06-26 12:08:48,258 calibrate.py _nudge_pos():1806 [1] 686: 0.100 -0.0034270 0.0018500 8392 28.00 -18.132 12.244 2006-10-18T09:22:00.154681088 INFO 2025-06-26 12:08:48,749 calibrate.py _nudge_pos():1806 [1] 733: 0.110 -0.0005118 0.0005685 2856 9.53 -7.955 11.053 2006-10-18T09:32:18.142346240 INFO 2025-06-26 12:08:49,240 calibrate.py _nudge_pos():1806 [1] 780: 0.120 0.0000239 0.0004109 8226 27.43 0.129 2.776 2006-10-18T10:00:30.136436480 INFO 2025-06-26 12:08:49,733 calibrate.py _nudge_pos():1806 [1] 828: 0.120 -0.0000048 0.0005641 8730 29.11 -0.025 3.590 2006-10-18T10:30:24.143538688 INFO 2025-06-26 12:08:50,305 calibrate.py _nudge_pos():1806 [1] 883: 0.120 -0.0007600 -0.0008392 15772 52.60 -2.141 -2.957 2006-10-18T11:23:54.143638528 INFO 2025-06-26 12:08:50,781 calibrate.py _nudge_pos():1806 [1] 929: 0.130 -0.0010983 -0.0009189 13147 43.85 -3.712 -3.883 2006-10-18T12:08:30.140320256 INFO 2025-06-26 12:08:51,228 calibrate.py _nudge_pos():1806 [1] 971: 0.140 -0.0022737 -0.0013104 16617 55.41 -6.084 -4.382 2006-10-18T13:04:36.139733504 INFO 2025-06-26 12:08:51,729 calibrate.py _nudge_pos():1806 [1] 1018: 0.150 -0.0012951 -0.0010270 15327 51.13 -3.757 -3.722 2006-10-18T13:56:30.136410112 INFO 2025-06-26 12:08:52,213 calibrate.py _nudge_pos():1806 [1] 1064: 0.150 -0.0005905 -0.0003452 5443 18.15 -4.826 -3.524 2006-10-18T14:15:24.138725632 INFO 2025-06-26 12:08:52,538 calibrate.py _nudge_pos():1862 [1] 1073: - - - 5 0.01 - - INFO 2025-06-26 12:08:52,538 calibrate.py _nudge_pos():1868 [1] Points in final series = 231755 WARNING 2025-06-26 12:09:00,509 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:09:23,547 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 185490 INFO 2025-06-26 12:09:24,989 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:09:38,157 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:09:39,564 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:09:39,567 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.291.03/ctd1.nc INFO 2025-06-26 12:09:39,568 calibrate.py _range_qc_combined_nc():898 [1] Setting 123 ctd1_salinity values to NaN INFO 2025-06-26 12:09:39,569 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 12:09:39,569 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:09:49,648 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:09:51,048 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:09:51,051 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.291.03/ctd2.nc INFO 2025-06-26 12:09:51,052 calibrate.py _range_qc_combined_nc():898 [1] Setting 124 ctd2_salinity values to NaN INFO 2025-06-26 12:09:51,053 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 12:09:51,053 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:09:51,119 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:09:53,333 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 2784120 2784121 2784122] INFO 2025-06-26 12:09:53,765 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:09:53,771 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 12:09:53,771 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.291.03 ERROR 2025-06-26 12:09:53,771 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.291.03 INFO 2025-06-26 12:09:53,947 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_cal.nc INFO 2025-06-26 12:10:08,431 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 12:10:08,435 process.py align():251 [1] Alignment steps for 2006.291.03 INFO 2025-06-26 12:10:08,475 align.py process_cal():139 [1] Processing dorado_2006.291.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.291.03 INFO 2025-06-26 12:10:08,536 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:10:08,543 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:10:08,685 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:10:08,694 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:10:08,836 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:10:08,845 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:10:08,935 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:10:08,935 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:10:08,991 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:10:09,000 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:10:09,142 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:10:09,150 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:09,274 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:10:09,281 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:09,406 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:10:09,414 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:09,539 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:09,546 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:09,677 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:09,685 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:09,811 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:09,818 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:09,942 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:09,950 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:10,083 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:10,090 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:10,213 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:10,221 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:10,345 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:10,354 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:10,481 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:10,489 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:10,619 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:10,626 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:10,758 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:10,764 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:10,890 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:10,897 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:11,024 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:11,033 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:11,160 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:11,169 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:11,295 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:11,303 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:11,429 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:11,436 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:11,562 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:11,570 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:11,695 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.291.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:10:11,702 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:10:11,859 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:10:11,962 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:10:12,068 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:10:12,177 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:10:12,290 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:10:12,387 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_align.nc INFO 2025-06-26 12:10:12,510 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 12:10:12,513 process.py resample():273 [1] Resampling steps for 2006.291.03 INFO 2025-06-26 12:10:12,513 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:10:12,544 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_align.nc mission netCDF file INFO 2025-06-26 12:10:12,552 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_align.nc mission netCDF file INFO 2025-06-26 12:10:12,554 resample.py get_mission_start_end():1145 [1] navigation: 2006-10-18T01:22:36.895099392 to 2006-10-18T14:15:55.166599936 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 12:10:12,556 resample.py get_mission_start_end():1145 [1] hs2 : 2006-10-18T01:22:20.506222336 to 2006-10-18T14:15:55.216596480 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:10:12,559 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-10-18T01:22:35.115221248 to 2006-10-18T14:15:55.176599552 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 12:10:12,561 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-10-18T01:22:35.065224960 to 2006-10-18T14:15:55.056607744 (0 days 00:00:00.159988736 before mission_end) INFO 2025-06-26 12:10:12,563 resample.py get_mission_start_end():1145 [1] isus : 2006-10-18T01:23:39.260827136 to 2006-10-18T14:15:55.166599936 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 12:10:12,564 resample.py get_mission_start_end():1145 [1] biolume : 2006-10-18T01:22:15.296544768 to 2006-10-18T14:15:53.776661248 (0 days 00:00:01.439935232 before mission_end) INFO 2025-06-26 12:10:12,567 resample.py get_mission_start_end():1145 [1] tailcone : 2006-10-18T01:22:14.736617216 to 2006-10-18T14:15:55.086605568 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 12:10:12,568 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_align.nc mission netCDF file INFO 2025-06-26 12:10:12,568 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,052 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,132 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,209 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,285 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,351 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,416 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,480 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,544 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,606 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,666 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,727 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,787 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,848 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,909 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:13,970 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,032 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,096 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,158 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,219 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,282 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,344 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,406 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,431 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,454 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,476 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,501 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,573 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:10:14,940 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_1S.nc INFO 2025-06-26 12:10:19,014 create_products.py gulper_odv():401 [1] No gulper times found for 2006.291.03 INFO 2025-06-26 12:10:19,015 process.py archive():337 [1] Archiving steps for 2006.291.03 INFO 2025-06-26 12:10:19,015 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03, BASE_PATH = /data/auv_data INFO 2025-06-26 12:10:19,016 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 12:10:19,017 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.291.03_1S.nc INFO 2025-06-26 12:10:19,052 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:10:19,053 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.291.03_cal.nc INFO 2025-06-26 12:10:19,251 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:10:19,253 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.291.03_align.nc INFO 2025-06-26 12:10:19,428 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:10:19,482 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,528 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,533 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,567 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,709 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,718 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,786 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,823 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,948 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006291/2006.291.03 done. INFO 2025-06-26 12:10:19,948 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:10:19,949 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.291.03/dorado_2006.291.03_processing.log /Volumes/AUVCTD/surveys/2006/netcdf