INFO 2025-06-26 12:02:22,644 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 12:02:22,644 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Standard Biolume run. CTD1 was noisey - ctdToUse = ctd1 INFO 2025-06-26 12:02:22,644 process.py process_mission():449 [1] Processing BIOLUME mission 2006.270.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:02:22,644 process.py download_process():165 [1] Download and processing steps for 2006.270.00 INFO 2025-06-26 12:02:22,644 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006270/2006.270.00 INFO 2025-06-26 12:02:22,644 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006270/2006.270.00 to /data/auv_data/dorado/missionlogs/2006.270.00 INFO 2025-06-26 12:02:28,962 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.270.00 INFO 2025-06-26 12:02:28,963 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/ctdDriver.log (15763395 bytes) INFO 2025-06-26 12:02:30,080 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.270.00/ctdDriver.log: [ 107 1542 1964 2303 3056 3225 4119 7213 7951 10268 10992 11256 12144 13081 14137 26248 29022 29084 29350 32733 41749 44093 52436 107684 111832 112428 112919 120421 126795 133077 142924 166437] INFO 2025-06-26 12:02:30,126 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/ctdDriver2.log (15774829 bytes) INFO 2025-06-26 12:02:31,266 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.270.00/ctdDriver2.log: [ 6 868 2092 3352 3473 4902 7341 8658 10339 12910 13154 15520 19612 19697 27700 29410 29479 35794 41880 52566 68044 75545 83132 89829 105570 120550 126926 134395 141120 143055 154965 159455 166567 172464 177367] INFO 2025-06-26 12:02:31,326 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/gps.log (253436 bytes) INFO 2025-06-26 12:02:31,361 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/hydroscatlog.log (10757054 bytes) INFO 2025-06-26 12:02:32,616 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.270.00/hydroscatlog.log: [ 124 273 645 844 932 1126 1135 1579 1714 2188 2453 2527 3463 5377 5763 6018 6490 7689 11488 12367 13877 14710 16010 17458 23830 23963 26469 29569 31521 32953 35062 49004 51185 62244 68118 69420 74803 83111 87655 89890 90607 105598 112013 118289 120598 123936 124851 128099 138154 140571 141156 149040 152374 154995 156917 156992 169413 176510] INFO 2025-06-26 12:02:32,653 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/navigation.log (52854450 bytes) INFO 2025-06-26 12:02:36,605 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/isuslog.log (1077429 bytes) INFO 2025-06-26 12:02:36,709 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.270.00/isuslog.log: [1 2 3 4 5 6 7 9] INFO 2025-06-26 12:02:36,713 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/parosci.log (23004998 bytes) INFO 2025-06-26 12:02:38,601 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.270.00/parosci.log: [ 1 2 3 4 7 8 9 16 17 34 35 39 40 82 83 225 226 369 370 652 741 812 860 861 925 997 1382 1411 1443 2008 2009 2063 2294 2295 2347 2348 2528 2615 2637 2638 2747 2907 2961 3041 3042 3089 3679 4112 4248 4250 4536 5215 5309 5310 5659 6007 6008 6578 6579 6580 7784 7786 7971 7972 8208 8209 8505 8784 8785 8786 9232 9233 9234 9271 10135 10136 11621 12893 12894 13157 13374 13786 13787 13788 13840 13842 13843 15184 15185 17353 17354 20556 20752 20753 21454 23406 23827 23828 27898 28642 29863 29979 30684 30685 30706 31120 31121 32246 34768 37101 38383 38384 42797 42799 52187 52188 52680 52681 59251 59252 59254 61811 64067 65265 69991 74310 78180 79054 81872 84870 84871 88105 88549 93750 93751 101939 111630 111632 113680 113682 114194 114195 122011 122314 143768 146791 146792 157371 157372 157373 157374 158360 158362 160346 162125 162127 166469 172456 172457 174631 174632 182181 184964 196463 196464 198378 198380 201061 201062 202234 207499 207500 207696 210049 210051 210829 217384 217385 217386 217387 219821 219822 222279 222281 222282 228091 228092 230180 234427 240401 242314 242315 242316 244752 244754 260231 260232 274390 276645 282384 282386 282453 301106 301107 302421 302422 307535 307536 330019 333823 334812 334813 336596 336597 342202 342203 350372 359431 364804 373884 373885 375824 375825 379505 380627 380629 394512 397455 397457 398460 398461 402597 402598 407374 410044 410045 419515 419516 422638 426378 452922 452923 452924 453742 453743 462140 462263 462264 462713 462714 463205 463206 463208 464380 471885 471887 471888 474231 474232 478114 478115] INFO 2025-06-26 12:02:38,672 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/tailCone.log (10741627 bytes) INFO 2025-06-26 12:02:40,039 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.270.00/biolume.log (12201516 bytes) INFO 2025-06-26 12:02:41,256 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:02:41,879 logs2netcdfs.py download_process_logs():807 [1] Time to process: 12.92 seconds WARNING 2025-06-26 12:02:41,879 process.py download_process():196 [1] No lopc.bin file for 2006.270.00 INFO 2025-06-26 12:02:41,879 process.py calibrate():227 [1] Calibration steps for 2006.270.00 INFO 2025-06-26 12:02:42,187 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 12:02:42,189 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:02:42,945 calibrate.py _nudge_pos():1806 [1] 93: 0.170 -0.0003843 0.0003990 2153 7.23 -7.904 10.225 2006-09-27T01:44:29.206200320 INFO 2025-06-26 12:02:43,424 calibrate.py _nudge_pos():1806 [1] 141: 0.180 -0.0018922 -0.0014944 5595 18.71 -15.035 -14.798 2006-09-27T02:03:59.206049792 INFO 2025-06-26 12:02:43,947 calibrate.py _nudge_pos():1806 [1] 192: 0.190 -0.0038979 -0.0028058 10297 34.36 -16.861 -15.130 2006-09-27T02:39:11.201368320 INFO 2025-06-26 12:02:44,407 calibrate.py _nudge_pos():1806 [1] 237: 0.200 -0.0039687 -0.0024825 9403 31.36 -18.804 -14.667 2006-09-27T03:11:17.209427712 INFO 2025-06-26 12:02:44,857 calibrate.py _nudge_pos():1806 [1] 281: 0.190 -0.0044175 -0.0028476 10756 35.88 -18.290 -14.706 2006-09-27T03:47:53.208991232 INFO 2025-06-26 12:02:45,316 calibrate.py _nudge_pos():1806 [1] 326: 0.010 -0.0032758 0.0007477 9017 30.06 -16.182 4.609 2006-09-27T04:18:41.402381312 INFO 2025-06-26 12:02:45,724 calibrate.py _nudge_pos():1806 [1] 366: 0.020 -0.0025204 0.0017379 7003 23.35 -16.028 13.794 2006-09-27T04:42:41.403734784 INFO 2025-06-26 12:02:46,160 calibrate.py _nudge_pos():1806 [1] 409: 0.010 -0.0007908 0.0009999 2579 8.60 -13.657 21.553 2006-09-27T04:51:59.405509120 INFO 2025-06-26 12:02:46,585 calibrate.py _nudge_pos():1806 [1] 450: 0.020 -0.0039909 0.0043559 7298 24.33 -24.345 33.175 2006-09-27T05:16:59.402752256 INFO 2025-06-26 12:02:47,042 calibrate.py _nudge_pos():1806 [1] 494: 0.030 -0.0040591 0.0042056 6954 23.18 -25.983 33.619 2006-09-27T05:40:53.404516096 INFO 2025-06-26 12:02:47,475 calibrate.py _nudge_pos():1806 [1] 536: 0.020 -0.0049182 0.0047952 9002 30.01 -24.306 29.605 2006-09-27T06:11:35.408330240 INFO 2025-06-26 12:02:47,917 calibrate.py _nudge_pos():1806 [1] 579: 0.030 -0.0036787 0.0035270 10497 35.00 -15.586 18.675 2006-09-27T06:47:17.401593600 INFO 2025-06-26 12:02:48,365 calibrate.py _nudge_pos():1806 [1] 622: 0.030 -0.0037224 0.0020524 9116 30.40 -18.151 12.512 2006-09-27T07:18:23.403763712 INFO 2025-06-26 12:02:48,835 calibrate.py _nudge_pos():1806 [1] 667: 0.030 -0.0042742 0.0020201 9943 33.16 -19.097 11.287 2006-09-27T07:52:17.404425216 INFO 2025-06-26 12:02:49,247 calibrate.py _nudge_pos():1806 [1] 706: 0.030 -0.0032220 0.0016208 7546 25.16 -18.967 11.935 2006-09-27T08:18:05.408379648 INFO 2025-06-26 12:02:49,724 calibrate.py _nudge_pos():1806 [1] 752: 0.030 -0.0005238 0.0005392 2594 8.65 -8.972 11.555 2006-09-27T08:27:29.409742848 INFO 2025-06-26 12:02:50,158 calibrate.py _nudge_pos():1806 [1] 793: 0.040 -0.0000130 0.0006412 7895 26.33 -0.073 4.513 2006-09-27T08:54:29.408765440 INFO 2025-06-26 12:02:50,627 calibrate.py _nudge_pos():1806 [1] 838: 0.040 -0.0000783 0.0006450 8413 28.06 -0.413 4.259 2006-09-27T09:23:17.410389248 INFO 2025-06-26 12:02:51,130 calibrate.py _nudge_pos():1806 [1] 883: 0.050 -0.0001975 -0.0000742 16814 56.06 -0.522 -0.245 2006-09-27T10:20:05.406925312 INFO 2025-06-26 12:02:51,573 calibrate.py _nudge_pos():1806 [1] 925: 0.050 -0.0006207 -0.0005748 15566 51.91 -1.772 -2.052 2006-09-27T11:12:41.410724352 INFO 2025-06-26 12:02:52,047 calibrate.py _nudge_pos():1806 [1] 970: 0.080 -0.0016899 -0.0008578 17831 59.46 -4.214 -2.673 2006-09-27T12:12:53.403286016 INFO 2025-06-26 12:02:52,536 calibrate.py _nudge_pos():1806 [1] 1016: 0.070 -0.0007963 -0.0005457 14889 49.65 -2.379 -2.037 2006-09-27T13:03:17.406127360 INFO 2025-06-26 12:02:53,108 calibrate.py _nudge_pos():1806 [1] 1069: 0.080 -0.0003823 -0.0002192 5467 18.23 -3.111 -2.228 2006-09-27T13:22:23.407621120 INFO 2025-06-26 12:03:19,125 calibrate.py _nudge_pos():1806 [1] 3477: 0.090 -0.0000149 0.0000212 20 0.06 -34.839 62.153 2006-09-27T14:02:34.402456576 INFO 2025-06-26 12:03:19,288 calibrate.py _nudge_pos():1806 [1] 3491: 0.090 -0.0000194 0.0000505 15 0.05 -61.627 200.451 2006-09-27T14:02:50.401360384 INFO 2025-06-26 12:03:19,465 calibrate.py _nudge_pos():1862 [1] 3486: - - - 2 0.00 - - INFO 2025-06-26 12:03:19,465 calibrate.py _nudge_pos():1868 [1] Points in final series = 223904 WARNING 2025-06-26 12:03:27,296 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:03:51,097 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:04:04,149 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 60 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:04:05,475 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 60 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:04:05,479 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.270.00/ctd1.nc INFO 2025-06-26 12:04:05,480 calibrate.py _range_qc_combined_nc():898 [1] Setting 100 ctd1_salinity values to NaN INFO 2025-06-26 12:04:05,481 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 12:04:05,481 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:04:15,290 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:04:16,615 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:04:16,619 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.270.00/ctd2.nc INFO 2025-06-26 12:04:16,620 calibrate.py _range_qc_combined_nc():898 [1] Setting 90 ctd2_salinity values to NaN INFO 2025-06-26 12:04:16,620 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 12:04:16,621 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:04:18,244 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:04:20,317 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 2649484 2649485 2683620] INFO 2025-06-26 12:04:20,716 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:04:20,723 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 12:04:20,723 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.270.00 ERROR 2025-06-26 12:04:20,723 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.270.00 INFO 2025-06-26 12:04:20,893 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_cal.nc INFO 2025-06-26 12:04:34,841 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 12:04:34,845 process.py align():251 [1] Alignment steps for 2006.270.00 INFO 2025-06-26 12:04:34,883 align.py process_cal():139 [1] Processing dorado_2006.270.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.270.00 INFO 2025-06-26 12:04:34,941 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:04:34,948 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:04:35,091 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:04:35,099 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:04:35,237 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:04:35,246 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:04:35,334 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:04:35,335 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:04:35,390 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:04:35,398 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:04:35,534 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:04:35,542 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:35,664 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:04:35,672 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:35,793 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:04:35,800 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:35,921 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:35,928 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,052 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,060 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,180 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,187 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,309 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,317 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,439 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,447 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,569 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,576 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,698 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,705 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,830 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,837 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:36,956 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:36,963 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:37,087 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:37,097 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:37,227 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:37,235 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:37,358 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:37,365 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:37,487 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:37,495 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:37,616 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:37,623 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:37,745 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:37,753 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:37,876 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:37,883 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:38,004 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.270.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:04:38,011 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:04:38,163 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:04:38,264 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:04:38,366 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:04:38,473 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:04:38,587 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:04:38,682 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_align.nc INFO 2025-06-26 12:04:38,805 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 12:04:38,807 process.py resample():273 [1] Resampling steps for 2006.270.00 INFO 2025-06-26 12:04:38,808 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:04:38,838 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_align.nc mission netCDF file INFO 2025-06-26 12:04:38,846 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_align.nc mission netCDF file INFO 2025-06-26 12:04:38,848 resample.py get_mission_start_end():1145 [1] navigation: 2006-09-27T01:36:05.220725760 to 2006-09-27T14:03:06.810236416 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:04:38,850 resample.py get_mission_start_end():1145 [1] hs2 : 2006-09-27T01:35:48.501871104 to 2006-09-27T14:03:06.680245504 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 12:04:38,852 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-09-27T01:36:44.658024192 to 2006-09-27T14:03:06.740241408 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 12:04:38,854 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-09-27T01:36:12.760209408 to 2006-09-27T14:03:06.800237056 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 12:04:38,856 resample.py get_mission_start_end():1145 [1] isus : 2006-09-27T01:36:46.417903360 to 2006-09-27T14:03:05.910298112 (0 days 00:00:00.899938304 before mission_end) INFO 2025-06-26 12:04:38,858 resample.py get_mission_start_end():1145 [1] biolume : 2006-09-27T01:35:44.192132096 to 2006-09-27T14:03:05.980259072 (0 days 00:00:00.829977344 before mission_end) INFO 2025-06-26 12:04:38,860 resample.py get_mission_start_end():1145 [1] tailcone : 2006-09-27T01:35:43.752196352 to 2006-09-27T14:03:06.770239232 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 12:04:38,861 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_align.nc mission netCDF file INFO 2025-06-26 12:04:38,861 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,330 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,407 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,483 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,558 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,623 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,686 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,750 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,812 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,872 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,931 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:39,992 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,056 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,117 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,175 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,233 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,291 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,353 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,417 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,480 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,542 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,605 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,666 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,691 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,713 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,735 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,762 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:40,832 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:04:41,188 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_1S.nc INFO 2025-06-26 12:04:44,050 create_products.py gulper_odv():401 [1] No gulper times found for 2006.270.00 INFO 2025-06-26 12:04:44,051 process.py archive():337 [1] Archiving steps for 2006.270.00 INFO 2025-06-26 12:04:44,051 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00, BASE_PATH = /data/auv_data INFO 2025-06-26 12:04:44,052 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 12:04:44,054 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.270.00_1S.nc INFO 2025-06-26 12:04:44,088 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:04:44,089 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.270.00_cal.nc INFO 2025-06-26 12:04:44,269 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:04:44,271 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.270.00_align.nc INFO 2025-06-26 12:04:44,436 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:04:44,480 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,526 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,531 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,560 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,692 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,700 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,764 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,799 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,931 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006270/2006.270.00 done. INFO 2025-06-26 12:04:44,931 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:04:44,931 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.270.00/dorado_2006.270.00_processing.log /Volumes/AUVCTD/surveys/2006/netcdf