INFO 2025-06-26 11:43:19,894 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 11:43:19,895 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - as part of MB06 - Standard C1 to M2 and back - ctdToUse = ctd1 INFO 2025-06-26 11:43:19,895 process.py process_mission():449 [1] Processing BIOLUME mission 2006.227.09 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:43:19,895 process.py download_process():165 [1] Download and processing steps for 2006.227.09 INFO 2025-06-26 11:43:19,895 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006227/2006.227.09 INFO 2025-06-26 11:43:19,895 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006227/2006.227.09 to /data/auv_data/dorado/missionlogs/2006.227.09 INFO 2025-06-26 11:43:26,256 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.227.09 INFO 2025-06-26 11:43:26,256 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/ctdDriver.log (23220603 bytes) INFO 2025-06-26 11:43:28,029 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.09/ctdDriver.log: [ 6 402 659 2461 2476 2520 3184 4827 5601 5712 8674 17329 19113 20097 21630 30816 46084 47106 86003 95575 95708 131128 168403 173796 176985 177489 200748 215682 217052 239104 259126 259503] INFO 2025-06-26 11:43:28,105 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/ctdDriver2.log (23220597 bytes) INFO 2025-06-26 11:43:29,902 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.09/ctdDriver2.log: [ 29 401 403 1493 2093 2237 5010 5676 7511 9733 25775 30192 41649 46085 58216 65713 73214 82076 103024 103324 110144 118613 150588 157816 176985 177928 181647 195835 208186 215682 221958 230685 240830 241615 253961 259126 259503 260674] INFO 2025-06-26 11:43:30,013 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/gps.log (310316 bytes) INFO 2025-06-26 11:43:30,057 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/hydroscatlog.log (15831074 bytes) INFO 2025-06-26 11:43:31,943 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.09/hydroscatlog.log: [ 929 1013 2537 4181 5142 5695 7403 7603 8731 8767 9157 11364 17277 26007 41737 54257 60099 62568 72559 80781 86803 103265 104078 118662 137092 138727 143774 150621 160553 163221 165022 170715 178212 185704 186121 188030 213468 218588 222585 233342 253111 253151 253940] INFO 2025-06-26 11:43:31,997 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/navigation.log (77825846 bytes) INFO 2025-06-26 11:43:37,634 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/isuslog.log (1586773 bytes) INFO 2025-06-26 11:43:37,792 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/parosci.log (33921542 bytes) INFO 2025-06-26 11:43:40,570 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.09/parosci.log: [ 16 26 27 306 699 700 1381 2050 2053 2291 2747 2748 2900 2901 2902 3066 3067 4112 4261 4387 5883 6245 6862 7332 7333 9232 9233 9235 9236 9260 11281 11282 13687 13688 13789 13840 13841 15431 15473 16394 16395 20752 20753 23168 24558 31121 34323 34733 34734 36459 41957 46283 55013 55170 64334 65764 69243 69627 69989 77012 79926 84790 90582 90583 94018 103651 104976 115942 115943 131541 135990 135991 140835 148668 148669 156059 156060 184201 184202 196197 206880 206882 254203 256369 277777 277778 279739 310096 313152 319564 323429 323430 332197 336718 356798 360882 362905 363216 367120 367121 367122 370306 371509 371511 376897 376899 396991 400800 410812 435367 437156 441995 441996 454502 457253 465567 497425 498192 498193 500911 503675 503676 512185 512186 541779 541883 541884 547419 558944 558945 596281 597868 597869 603280 614264 617929 617930 620691 629264 652600 656013 656014 669508 669509 672955 693883 694036 694037] INFO 2025-06-26 11:43:40,665 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/tailCone.log (15820939 bytes) INFO 2025-06-26 11:43:42,689 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.09/biolume.log (17955676 bytes) INFO 2025-06-26 11:43:44,391 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:43:45,319 logs2netcdfs.py download_process_logs():807 [1] Time to process: 19.06 seconds WARNING 2025-06-26 11:43:45,319 process.py download_process():196 [1] No lopc.bin file for 2006.227.09 INFO 2025-06-26 11:43:45,319 process.py calibrate():227 [1] Calibration steps for 2006.227.09 INFO 2025-06-26 11:43:45,797 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 11:43:45,799 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:43:46,609 calibrate.py _nudge_pos():1806 [1] 93: 0.190 -0.0003001 0.0000478 2217 7.41 -6.009 1.195 2006-08-15T20:29:40.975083008 INFO 2025-06-26 11:43:47,324 calibrate.py _nudge_pos():1806 [1] 161: 0.190 -0.0014316 0.0029791 12336 41.18 -5.161 13.405 2006-08-15T21:11:58.971218688 INFO 2025-06-26 11:43:47,937 calibrate.py _nudge_pos():1806 [1] 219: 0.190 0.0005877 -0.0005903 8770 29.25 2.984 -3.740 2006-08-15T21:42:10.977087488 INFO 2025-06-26 11:43:48,752 calibrate.py _nudge_pos():1806 [1] 296: 0.190 -0.0026258 -0.0013752 11226 37.43 -10.417 -6.808 2006-08-15T22:20:52.978019840 INFO 2025-06-26 11:43:49,473 calibrate.py _nudge_pos():1806 [1] 362: 0.190 -0.0021547 0.0002108 11733 39.11 -8.182 0.999 2006-08-15T23:01:04.972786688 INFO 2025-06-26 11:43:50,141 calibrate.py _nudge_pos():1806 [1] 424: 0.190 0.0000076 -0.0017071 8243 27.48 0.041 -11.513 2006-08-15T23:29:34.975643392 INFO 2025-06-26 11:43:50,465 calibrate.py _nudge_pos():1806 [1] 450: 0.200 -0.0000133 -0.0000200 30 0.10 -20.478 -38.265 2006-08-15T23:30:05.973520128 INFO 2025-06-26 11:43:50,898 calibrate.py _nudge_pos():1806 [1] 489: 0.020 0.0009842 -0.0015491 10813 36.05 4.055 -7.963 2006-08-16T00:06:47.172727296 INFO 2025-06-26 11:43:51,521 calibrate.py _nudge_pos():1806 [1] 546: 0.190 -0.0001660 -0.0038437 15257 50.86 -0.485 -14.004 2006-08-16T00:58:34.979828224 INFO 2025-06-26 11:43:52,115 calibrate.py _nudge_pos():1806 [1] 602: 0.020 0.0033318 0.0018298 13399 44.68 11.078 7.589 2006-08-16T01:44:11.172386048 INFO 2025-06-26 11:43:52,525 calibrate.py _nudge_pos():1806 [1] 640: 0.010 -0.0000023 -0.0000053 30 0.10 -3.485 -10.202 2006-08-16T01:44:54.179439872 INFO 2025-06-26 11:43:52,558 calibrate.py _nudge_pos():1806 [1] 643: 0.030 0.0031787 -0.0017240 13689 45.65 10.346 -6.999 2006-08-16T02:30:35.171668992 INFO 2025-06-26 11:43:53,352 calibrate.py _nudge_pos():1806 [1] 716: 0.010 0.0017279 -0.0066274 15268 50.90 5.044 -24.128 2006-08-16T03:22:41.177522944 INFO 2025-06-26 11:43:53,374 calibrate.py _nudge_pos():1806 [1] 718: 0.020 -0.0000113 0.0000783 35 0.11 -14.763 128.011 2006-08-16T03:22:49.176975104 INFO 2025-06-26 11:43:54,047 calibrate.py _nudge_pos():1806 [1] 780: 0.030 -0.0001431 -0.0008922 3788 12.63 -1.684 -13.090 2006-08-16T03:36:29.170801664 INFO 2025-06-26 11:43:54,409 calibrate.py _nudge_pos():1806 [1] 814: 0.010 0.0054156 -0.0041249 16663 55.55 14.485 -13.760 2006-08-16T04:32:35.180214272 INFO 2025-06-26 11:43:55,039 calibrate.py _nudge_pos():1806 [1] 872: 0.020 0.0032855 -0.0047246 16511 55.05 8.867 -15.904 2006-08-16T05:28:35.180038400 INFO 2025-06-26 11:43:55,641 calibrate.py _nudge_pos():1806 [1] 925: 0.030 0.0016602 -0.0036539 16596 55.33 4.457 -12.237 2006-08-16T06:24:47.179040768 INFO 2025-06-26 11:43:56,290 calibrate.py _nudge_pos():1806 [1] 982: 0.030 -0.0000105 -0.0017893 13907 46.36 -0.034 -7.151 2006-08-16T07:12:05.174624768 INFO 2025-06-26 11:43:57,015 calibrate.py _nudge_pos():1806 [1] 1046: 0.040 0.0000565 -0.0016916 6253 20.85 0.402 -15.036 2006-08-16T07:33:59.174609408 INFO 2025-06-26 11:43:57,643 calibrate.py _nudge_pos():1806 [1] 1101: 0.040 0.0006432 -0.0008508 11485 38.30 2.494 -4.117 2006-08-16T08:13:11.173486592 INFO 2025-06-26 11:43:58,333 calibrate.py _nudge_pos():1806 [1] 1160: 0.050 0.0009346 -0.0004271 11407 38.03 3.649 -2.081 2006-08-16T08:52:11.173185536 INFO 2025-06-26 11:43:58,988 calibrate.py _nudge_pos():1806 [1] 1218: 0.050 0.0004640 0.0006385 11410 38.05 1.811 3.110 2006-08-16T09:31:11.172884480 INFO 2025-06-26 11:43:59,635 calibrate.py _nudge_pos():1806 [1] 1274: 0.050 0.0003860 0.0011401 11303 37.68 1.521 5.607 2006-08-16T10:09:47.174227456 INFO 2025-06-26 11:44:00,339 calibrate.py _nudge_pos():1806 [1] 1330: 0.050 0.0005391 0.0020965 11152 37.18 2.153 10.449 2006-08-16T10:47:53.177625600 INFO 2025-06-26 11:44:00,945 calibrate.py _nudge_pos():1806 [1] 1383: 0.050 0.0002784 0.0013502 11167 37.23 1.110 6.720 2006-08-16T11:25:59.171024384 INFO 2025-06-26 11:44:01,518 calibrate.py _nudge_pos():1806 [1] 1434: 0.040 -0.0002856 0.0009197 11596 38.66 -1.096 4.408 2006-08-16T12:05:29.178667776 INFO 2025-06-26 11:44:02,104 calibrate.py _nudge_pos():1806 [1] 1485: 0.050 -0.0000747 0.0005409 4938 16.46 -0.673 6.088 2006-08-16T12:22:47.177559808 INFO 2025-06-26 11:44:02,662 calibrate.py _nudge_pos():1806 [1] 1534: 0.070 -0.0001538 0.0014465 10498 35.00 -0.652 7.659 2006-08-16T12:58:35.170412288 INFO 2025-06-26 11:44:03,189 calibrate.py _nudge_pos():1806 [1] 1581: 0.050 0.0003122 0.0012776 8079 26.93 1.720 8.791 2006-08-16T13:26:17.176557056 INFO 2025-06-26 11:44:03,789 calibrate.py _nudge_pos():1806 [1] 1634: 0.060 0.0001369 0.0013092 8739 29.13 0.697 8.328 2006-08-16T13:56:17.173248768 INFO 2025-06-26 11:44:33,596 calibrate.py _nudge_pos():1862 [1] 4276: - - - 3 0.01 - - INFO 2025-06-26 11:44:33,597 calibrate.py _nudge_pos():1868 [1] Points in final series = 329642 WARNING 2025-06-26 11:44:45,055 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:45:20,002 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:45:38,564 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:45:40,514 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:45:40,518 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.227.09/ctd1.nc INFO 2025-06-26 11:45:40,520 calibrate.py _range_qc_combined_nc():898 [1] Setting 42 ctd1_salinity values to NaN INFO 2025-06-26 11:45:40,521 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 11:45:40,521 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:45:54,963 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:45:56,948 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:45:56,952 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.227.09/ctd2.nc INFO 2025-06-26 11:45:56,953 calibrate.py _range_qc_combined_nc():898 [1] Setting 43 ctd2_salinity values to NaN INFO 2025-06-26 11:45:56,954 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 11:45:56,954 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:45:57,048 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:46:00,089 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3953171 3953172 3960120] INFO 2025-06-26 11:46:00,707 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:46:00,714 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 11:46:00,715 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.227.09 ERROR 2025-06-26 11:46:00,715 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.227.09 INFO 2025-06-26 11:46:00,967 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_cal.nc INFO 2025-06-26 11:46:21,505 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 11:46:21,513 process.py align():251 [1] Alignment steps for 2006.227.09 INFO 2025-06-26 11:46:21,557 align.py process_cal():139 [1] Processing dorado_2006.227.09_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.227.09 INFO 2025-06-26 11:46:21,641 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:46:21,650 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:46:21,862 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:46:21,874 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:46:22,075 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:46:22,086 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:46:22,278 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:46:22,279 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:46:22,359 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:46:22,370 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:46:22,577 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:46:22,588 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:22,766 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:46:22,776 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:22,953 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:46:22,962 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:23,139 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:23,151 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:23,329 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:23,338 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:23,513 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:23,523 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:23,698 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:23,708 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:23,879 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:23,889 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:24,063 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:24,073 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:24,246 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:24,257 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:24,432 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:24,442 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:24,617 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:24,626 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:24,802 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:24,810 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:24,985 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:24,994 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:25,170 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:25,180 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:25,353 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:25,364 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:25,538 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:25,549 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:25,739 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:25,749 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:25,924 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:25,935 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:26,111 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.09_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:46:26,120 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:46:26,345 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:46:26,493 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:46:26,637 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:46:26,789 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:46:26,948 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 11:46:27,080 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_align.nc INFO 2025-06-26 11:46:27,237 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 11:46:27,239 process.py resample():273 [1] Resampling steps for 2006.227.09 INFO 2025-06-26 11:46:27,240 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:46:27,275 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_align.nc mission netCDF file INFO 2025-06-26 11:46:27,284 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_align.nc mission netCDF file INFO 2025-06-26 11:46:27,286 resample.py get_mission_start_end():1145 [1] navigation: 2006-08-15T20:21:06.470329088 to 2006-08-16T14:40:40.770779904 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 11:46:27,289 resample.py get_mission_start_end():1145 [1] hs2 : 2006-08-15T20:20:49.611484160 to 2006-08-16T14:40:40.830775808 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:46:27,291 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-08-15T20:21:12.939885824 to 2006-08-16T14:40:40.670786816 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 11:46:27,294 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-08-15T20:21:12.969883904 to 2006-08-16T14:40:40.720783360 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 11:46:27,296 resample.py get_mission_start_end():1145 [1] isus : 2006-08-15T20:22:08.616071936 to 2006-08-16T14:40:39.840843776 (0 days 00:00:00.989932032 before mission_end) INFO 2025-06-26 11:46:27,298 resample.py get_mission_start_end():1145 [1] biolume : 2006-08-15T20:20:45.221750528 to 2006-08-16T14:40:39.790812672 (0 days 00:00:01.039963136 before mission_end) INFO 2025-06-26 11:46:27,300 resample.py get_mission_start_end():1145 [1] tailcone : 2006-08-15T20:20:45.061795584 to 2006-08-16T14:40:40.680786176 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 11:46:27,301 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_align.nc mission netCDF file INFO 2025-06-26 11:46:27,302 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:27,962 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,071 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,177 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,282 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,372 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,463 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,554 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,640 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,723 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,807 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,890 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:28,976 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,061 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,145 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,230 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,313 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,400 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,486 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,572 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,657 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,745 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,830 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,863 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,892 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,918 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:29,950 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:30,052 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:46:30,529 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_1S.nc INFO 2025-06-26 11:46:32,607 create_products.py gulper_odv():401 [1] No gulper times found for 2006.227.09 INFO 2025-06-26 11:46:32,607 process.py archive():337 [1] Archiving steps for 2006.227.09 INFO 2025-06-26 11:46:32,607 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09, BASE_PATH = /data/auv_data INFO 2025-06-26 11:46:32,609 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:46:32,610 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.227.09_1S.nc INFO 2025-06-26 11:46:32,656 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:46:32,657 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.227.09_cal.nc INFO 2025-06-26 11:46:32,911 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:46:32,912 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.227.09_align.nc INFO 2025-06-26 11:46:33,152 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:46:33,217 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,279 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,285 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,328 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,511 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,520 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,610 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,666 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,833 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.09 done. INFO 2025-06-26 11:46:33,833 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:46:33,834 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.09/dorado_2006.227.09_processing.log /Volumes/AUVCTD/surveys/2006/netcdf