INFO 2025-06-26 12:13:28,955 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 12:13:28,955 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - out to between M1 & M2 - ctdToUse = ctd1 INFO 2025-06-26 12:13:28,955 process.py process_mission():449 [1] Processing AUVCTD mission 2006.324.11 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:13:28,955 process.py download_process():165 [1] Download and processing steps for 2006.324.11 INFO 2025-06-26 12:13:28,955 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006324/2006.324.11 INFO 2025-06-26 12:13:28,955 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006324/2006.324.11 to /data/auv_data/dorado/missionlogs/2006.324.11 INFO 2025-06-26 12:13:35,128 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.324.11 INFO 2025-06-26 12:13:35,128 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/ctdDriver.log (21933955 bytes) INFO 2025-06-26 12:13:36,656 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.324.11/ctdDriver.log: [ 6 1000 9608 15119 55524 61973 85657 94362 109369 131458 133324 135652 139101 139348 155707 162513 163137 180996 191656 203269 207374 243912 249214] INFO 2025-06-26 12:13:36,719 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/ctdDriver2.log (21931749 bytes) INFO 2025-06-26 12:13:38,304 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.324.11/ctdDriver2.log: [ 999 3395 9605 15116 22463 46126 55522 60076 116244 131839 135595 135644 143315 163121 199265 203249 241108 243866 249189] INFO 2025-06-26 12:13:38,378 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/gps.log (157676 bytes) INFO 2025-06-26 12:13:38,403 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/hydroscatlog.log (14970614 bytes) INFO 2025-06-26 12:13:40,139 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.324.11/hydroscatlog.log: [ 6456 14584 19237 19569 24953 46093 47499 69380 69381 75704 85813 94007 94627 97687 102040 102774 105851 109460 114974 123948 125475 127224 132026 133202 135832 139284 139285 142330 143193 145225 153916 157365 159782 160570 161026 163342 169223 169691 174237 175102 176069 182356 184212 187930 189468 200749 202641 203500 207016 209189 210798 216919 217174 222008 222453 224409 224410 233098 237005 248635] INFO 2025-06-26 12:13:40,187 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/navigation.log (73574778 bytes) INFO 2025-06-26 12:13:46,159 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/isuslog.log (1497813 bytes) INFO 2025-06-26 12:13:46,308 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/parosci.log (32174582 bytes) INFO 2025-06-26 12:13:48,933 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.324.11/parosci.log: [ 1 29 227 1282 1307 1381 2747 3000 4112 5949 6356 6826 6827 6933 7968 8901 9232 9265 13229 13322 13800 13840 19968 20752 21125 23019 29926 31120 32486 39283 39284 41000 52626 61690 63975 67092 67094 68429 69770 70318 77200 77201 88393 88394 101535 107946 107947 112944 113045 124287 127627 145030 146077 149514 156249 161902 164581 166523 166524 166902 181040 186388 186389 203334 203335 205193 205194 208272 208273 208274 210489 213647 213648 221598 221599 221757 230076 230448 232272 233757 233758 241480 251964 251965 251966 253847 253910 259802 262364 262365 274054 276019 276020 292993 292994 292995 293985 293986 295653 295655 295656 315587 315589 319835 326425 332943 334507 334508 337029 339344 339345 339347 341740 354648 356147 357813 357840 357841 363621 363622 364879 364880 374160 374161 374162 374780 374821 375264 375265 378953 378954 383035 383037 383038 383040 383041 384582 390124 394386 394993 406872 413497 413498 413499 415144 415145 422762 422763 432595 432597 435274 435276 435277 435747 446230 446231 451140 454629 454630 455440 455888 468091 468092 470800 473016 473017 473019 475584 475585 480386 486846 486848 486849 489922 489923 489924 502380 503665 503666 503668 504896 504897 504898 511225 514107 515885 516786 534598 534599 534600 538678 538680 538681 539360 539361 544441 544443 544444 557797 557798 557799 560597 560598 566367 566368 576349 576351 576352 578442 578443 578445 585491 585492 585494 596508 601488 601489 601491 604432 615068 615070 615071 622310 622312 622313 622397 622398 623693 623694 626289 626290 636773 636774 641450 642779 642780 645179 645181 646875 646877 649909 649910 649911 649912 655931 655989 655990 661871 667993] INFO 2025-06-26 12:13:49,025 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/tailCone.log (14954347 bytes) INFO 2025-06-26 12:13:50,855 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.324.11/biolume.log (16979196 bytes) INFO 2025-06-26 12:13:52,442 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:13:53,319 logs2netcdfs.py download_process_logs():807 [1] Time to process: 18.19 seconds WARNING 2025-06-26 12:13:53,320 process.py download_process():196 [1] No lopc.bin file for 2006.324.11 INFO 2025-06-26 12:13:53,320 process.py calibrate():227 [1] Calibration steps for 2006.324.11 INFO 2025-06-26 12:13:53,802 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 12:13:53,804 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:13:54,559 calibrate.py _nudge_pos():1806 [1] 89: 0.080 -0.0002369 0.0005818 3419 11.41 -3.082 9.446 2006-11-20T22:19:42.069919232 INFO 2025-06-26 12:13:55,265 calibrate.py _nudge_pos():1806 [1] 158: 0.090 0.0002203 0.0031070 15163 50.56 0.647 11.386 2006-11-20T23:11:24.067417856 INFO 2025-06-26 12:13:55,841 calibrate.py _nudge_pos():1806 [1] 215: 0.090 -0.0026503 0.0035002 9229 30.76 -12.792 21.083 2006-11-20T23:43:06.067121920 INFO 2025-06-26 12:13:56,532 calibrate.py _nudge_pos():1806 [1] 283: 0.100 -0.0039886 0.0049388 13281 44.28 -13.376 20.667 2006-11-21T00:28:30.070514944 INFO 2025-06-26 12:13:57,301 calibrate.py _nudge_pos():1806 [1] 357: 0.090 0.0012251 0.0042848 9804 32.68 5.567 24.295 2006-11-21T01:02:24.071176192 INFO 2025-06-26 12:13:57,864 calibrate.py _nudge_pos():1806 [1] 411: 0.110 -0.0022226 0.0047164 13712 45.71 -7.221 19.118 2006-11-21T01:49:00.069637376 INFO 2025-06-26 12:13:57,917 calibrate.py _nudge_pos():1806 [1] 416: 0.100 0.0000054 0.0000451 25 0.08 9.946 104.563 2006-11-21T01:49:09.069020928 INFO 2025-06-26 12:13:58,585 calibrate.py _nudge_pos():1806 [1] 481: 0.110 -0.0056088 0.0046948 15197 50.68 -16.437 17.166 2006-11-21T02:40:54.066313984 INFO 2025-06-26 12:13:59,183 calibrate.py _nudge_pos():1806 [1] 537: 0.110 -0.0049295 -0.0022917 13370 44.58 -16.425 -9.526 2006-11-21T03:26:24.069295872 INFO 2025-06-26 12:13:59,949 calibrate.py _nudge_pos():1806 [1] 609: 0.130 -0.0046097 0.0024370 13614 45.40 -15.085 9.947 2006-11-21T04:13:00.067756800 INFO 2025-06-26 12:14:00,491 calibrate.py _nudge_pos():1806 [1] 660: 0.140 -0.0064366 0.0054491 15193 50.66 -18.874 19.930 2006-11-21T05:04:30.066077440 INFO 2025-06-26 12:14:01,230 calibrate.py _nudge_pos():1806 [1] 727: 0.130 -0.0019798 0.0000644 3354 11.18 -26.310 1.067 2006-11-21T05:16:48.065521152 INFO 2025-06-26 12:14:01,954 calibrate.py _nudge_pos():1806 [1] 792: 0.130 -0.0003533 0.0054764 16408 54.73 -0.959 18.542 2006-11-21T06:12:36.066167296 INFO 2025-06-26 12:14:02,468 calibrate.py _nudge_pos():1806 [1] 838: 0.140 0.0020153 0.0045247 16474 54.95 5.448 15.259 2006-11-21T07:08:18.067224832 INFO 2025-06-26 12:14:03,108 calibrate.py _nudge_pos():1806 [1] 896: 0.140 0.0043867 0.0045460 16232 54.15 12.032 15.557 2006-11-21T08:03:24.070747904 INFO 2025-06-26 12:14:03,821 calibrate.py _nudge_pos():1806 [1] 963: 0.160 0.0051712 0.0055232 16313 54.40 14.118 18.814 2006-11-21T08:58:54.062627840 INFO 2025-06-26 12:14:04,541 calibrate.py _nudge_pos():1806 [1] 1028: 0.150 -0.0022849 0.0029591 6336 21.13 -16.060 25.950 2006-11-21T09:21:06.061379584 INFO 2025-06-26 12:14:05,254 calibrate.py _nudge_pos():1806 [1] 1094: 0.150 0.0029281 0.0070438 14344 47.83 9.091 27.289 2006-11-21T10:10:01.070317824 INFO 2025-06-26 12:14:06,003 calibrate.py _nudge_pos():1806 [1] 1164: 0.170 0.0019738 0.0045959 11101 37.03 7.915 22.998 2006-11-21T10:48:12.063374080 INFO 2025-06-26 12:14:06,716 calibrate.py _nudge_pos():1806 [1] 1227: 0.180 0.0021028 0.0051078 11201 37.36 8.356 25.332 2006-11-21T11:26:36.065539072 INFO 2025-06-26 12:14:07,330 calibrate.py _nudge_pos():1806 [1] 1283: 0.160 0.0030473 0.0043040 11359 37.88 11.943 21.054 2006-11-21T12:05:24.066060032 INFO 2025-06-26 12:14:07,995 calibrate.py _nudge_pos():1806 [1] 1344: 0.170 0.0029331 0.0028232 10224 34.10 12.770 15.343 2006-11-21T12:40:30.061789440 INFO 2025-06-26 12:14:08,651 calibrate.py _nudge_pos():1806 [1] 1404: 0.170 0.0018896 0.0032452 10796 36.01 7.788 16.698 2006-11-21T13:17:30.069708544 INFO 2025-06-26 12:14:09,256 calibrate.py _nudge_pos():1806 [1] 1458: 0.180 0.0020548 0.0022606 8849 29.51 10.334 14.193 2006-11-21T13:47:54.064756480 INFO 2025-06-26 12:14:09,919 calibrate.py _nudge_pos():1806 [1] 1518: 0.170 0.0012895 0.0011894 4862 16.21 11.805 13.594 2006-11-21T14:05:06.064059392 INFO 2025-06-26 12:14:10,557 calibrate.py _nudge_pos():1806 [1] 1576: 0.170 0.0013924 0.0026239 8890 29.65 6.970 16.400 2006-11-21T14:35:42.068284416 INFO 2025-06-26 12:14:11,201 calibrate.py _nudge_pos():1806 [1] 1635: 0.170 0.0009552 0.0024849 7652 25.53 5.552 18.036 2006-11-21T15:02:12.069362176 INFO 2025-06-26 12:14:11,855 calibrate.py _nudge_pos():1806 [1] 1695: 0.170 0.0004765 0.0014556 4711 15.71 4.499 17.165 2006-11-21T15:18:54.070720256 INFO 2025-06-26 12:14:17,190 calibrate.py _nudge_pos():1862 [1] 2156: - - - 0 0.00 - - INFO 2025-06-26 12:14:17,190 calibrate.py _nudge_pos():1868 [1] Points in final series = 311749 WARNING 2025-06-26 12:14:28,042 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:15:01,438 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:15:19,162 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:15:21,000 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:15:21,004 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.324.11/ctd1.nc INFO 2025-06-26 12:15:21,005 calibrate.py _range_qc_combined_nc():898 [1] Setting 4 ctd1_salinity values to NaN INFO 2025-06-26 12:15:21,006 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 12:15:21,006 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:15:34,622 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:15:36,491 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:15:36,495 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.324.11/ctd2.nc INFO 2025-06-26 12:15:36,497 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 12:15:36,497 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 12:15:36,497 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:15:36,586 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:15:39,448 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3744366 3744367 3744368] INFO 2025-06-26 12:15:40,059 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:15:40,066 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 12:15:40,066 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.324.11 ERROR 2025-06-26 12:15:40,066 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.324.11 INFO 2025-06-26 12:15:40,305 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_cal.nc INFO 2025-06-26 12:15:59,705 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 12:15:59,713 process.py align():251 [1] Alignment steps for 2006.324.11 INFO 2025-06-26 12:15:59,754 align.py process_cal():139 [1] Processing dorado_2006.324.11_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.324.11 INFO 2025-06-26 12:15:59,833 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:15:59,841 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:16:00,038 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:16:00,049 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:16:00,242 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:16:00,252 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:16:00,371 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:16:00,371 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:16:00,447 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:16:00,457 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 12:16:00,643 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:16:00,653 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:00,816 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:16:00,825 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:00,991 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:16:00,999 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:01,184 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:01,193 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:01,359 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:01,368 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:01,533 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:01,542 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:01,711 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:01,720 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:01,890 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:01,900 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:02,069 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:02,079 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:02,242 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:02,253 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:02,417 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:02,426 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:02,592 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:02,602 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:02,767 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:02,775 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:16:02,942 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:02,951 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:16:03,117 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:03,126 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:16:03,288 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:03,299 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:16:03,460 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:03,469 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:16:03,632 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:03,641 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:16:03,807 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:03,816 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:16:03,981 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.324.11_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:16:03,990 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:16:04,203 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:16:04,338 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:16:04,473 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:16:04,613 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:16:04,763 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:16:04,887 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_align.nc INFO 2025-06-26 12:16:05,038 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 12:16:05,040 process.py resample():273 [1] Resampling steps for 2006.324.11 INFO 2025-06-26 12:16:05,041 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:16:05,075 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_align.nc mission netCDF file INFO 2025-06-26 12:16:05,083 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_align.nc mission netCDF file INFO 2025-06-26 12:16:05,086 resample.py get_mission_start_end():1145 [1] navigation: 2006-11-20T22:07:11.461339392 to 2006-11-21T15:26:56.067700992 (0 days 00:00:00.169988608 before mission_end) INFO 2025-06-26 12:16:05,088 resample.py get_mission_start_end():1145 [1] hs2 : 2006-11-20T22:06:54.902473984 to 2006-11-21T15:26:56.127696896 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 12:16:05,091 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-11-20T22:07:18.450860800 to 2006-11-21T15:26:56.167694336 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 12:16:05,093 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-11-20T22:07:18.700843520 to 2006-11-21T15:26:56.047702528 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 12:16:05,095 resample.py get_mission_start_end():1145 [1] isus : 2006-11-20T22:08:18.046778112 to 2006-11-21T15:26:54.967776512 (0 days 00:00:01.269913088 before mission_end) INFO 2025-06-26 12:16:05,097 resample.py get_mission_start_end():1145 [1] biolume : 2006-11-20T22:06:50.322753536 to 2006-11-21T15:26:55.507705088 (0 days 00:00:00.729984512 before mission_end) INFO 2025-06-26 12:16:05,099 resample.py get_mission_start_end():1145 [1] tailcone : 2006-11-20T22:06:50.102802688 to 2006-11-21T15:26:56.237689600 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:16:05,100 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_align.nc mission netCDF file INFO 2025-06-26 12:16:05,101 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:05,720 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:05,822 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:05,922 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,022 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,107 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,191 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,274 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,356 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,433 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,515 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,594 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,671 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,747 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,824 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,900 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:06,978 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,060 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,145 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,226 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,309 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,390 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,471 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,504 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,529 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,554 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,584 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:07,676 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:16:08,125 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_1S.nc INFO 2025-06-26 12:16:10,415 create_products.py gulper_odv():401 [1] No gulper times found for 2006.324.11 INFO 2025-06-26 12:16:10,416 process.py archive():337 [1] Archiving steps for 2006.324.11 INFO 2025-06-26 12:16:10,416 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11, BASE_PATH = /data/auv_data INFO 2025-06-26 12:16:10,417 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 12:16:10,419 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.324.11_1S.nc INFO 2025-06-26 12:16:10,461 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:16:10,462 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.324.11_cal.nc INFO 2025-06-26 12:16:10,699 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:16:10,700 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.324.11_align.nc INFO 2025-06-26 12:16:10,923 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:16:10,988 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,048 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,053 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,095 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,275 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,285 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,369 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,422 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,584 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006324/2006.324.11 done. INFO 2025-06-26 12:16:11,584 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:16:11,584 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.324.11/dorado_2006.324.11_processing.log /Volumes/AUVCTD/surveys/2006/netcdf