INFO 2025-06-26 14:48:07,682 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 14:48:07,683 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Canyon transect - ctdToUse = ctd2 INFO 2025-06-26 14:48:07,683 process.py process_mission():449 [1] Processing AUVCTD mission 2009.125.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:48:07,683 process.py download_process():165 [1] Download and processing steps for 2009.125.00 INFO 2025-06-26 14:48:07,683 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009125/2009.125.00 INFO 2025-06-26 14:48:07,683 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009125/2009.125.00 to /data/auv_data/dorado/missionlogs/2009.125.00 INFO 2025-06-26 14:48:15,531 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.125.00 INFO 2025-06-26 14:48:15,532 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/ctdDriver.log (24876940 bytes) INFO 2025-06-26 14:48:17,458 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.125.00/ctdDriver.log: [ 105 130 311 450 654 733 1059 1221 1343 1415 2043 2425 2923 3295 3687 5179 6316 8391 8844 10579 11296 11654 15203 18402 19980 27731 29040 31212 36883 38898 42889 45624 53748 57423 57727 69503 73878 85844 86394 88099 106203 110013 110439 111299 123438 131331 136973 152107 157002 160100 176240 177540 182113 184686 186497 190566 192446 196711 197279 202142 218311 230843 245237 248807 253382 258107] INFO 2025-06-26 14:48:17,554 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/ctdDriver2.log (24885205 bytes) INFO 2025-06-26 14:48:19,464 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.125.00/ctdDriver2.log: [ 7 545 673 1010 3206 4799 5327 6076 7189 7760 7807 10677 11403 14140 17097 23921 24204 24667 24763 26560 29556 31305 34115 34884 38124 38417 38661 49694 59129 66626 67546 69834 75732 76440 89122 89971 90068 95304 104115 116068 123747 131000 134822 135759 141608 147043 151472 161435 163811 165330 165968 171945 177237 178719 187746 188139 209758 216190 219079 227192 230411 233397 237652 238740 242081 246566 253181 256182 257986 269061 271215 273079] INFO 2025-06-26 14:48:19,577 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/gps.log (165236 bytes) INFO 2025-06-26 14:48:19,605 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/hydroscatlog.log (23752954 bytes) INFO 2025-06-26 14:48:22,203 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.125.00/hydroscatlog.log: [ 2 96 114 309 498 928 935 1529 2354 3334 5299 5418 10775 24864 33794 37078 43050 49227 49794 52736 53940 57917 81166 90189 96355 104187 104365 105247 109592 111461 113264 123808 125328 129071 130915 131482 134160 137010 141658 143722 145128 152237 163850 171630 178751 179127 180666 190687 194113 201605 216205 216592 219092 222749 232357 233641 244635 258479 258851 259055 268365 269209 272175 273065] INFO 2025-06-26 14:48:22,305 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/navigation.log (83397570 bytes) INFO 2025-06-26 14:48:28,371 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/isuslog.log (1639349 bytes) INFO 2025-06-26 14:48:28,535 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.125.00/isuslog.log: [1 2 3 4 5 7 8] INFO 2025-06-26 14:48:28,540 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/parosci.log (28968710 bytes) INFO 2025-06-26 14:48:30,977 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/tailCone.log (3443323 bytes) INFO 2025-06-26 14:48:31,407 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/biolume.log (19244684 bytes) INFO 2025-06-26 14:48:33,234 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:48:34,236 logs2netcdfs.py download_process_logs():807 [1] Time to process: 18.70 seconds INFO 2025-06-26 14:48:34,237 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.125.00/lopc.bin (43068670 bytes) INFO 2025-06-26 14:48:34,237 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:48:34 2025 INFO 2025-06-26 14:48:34,237 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.125.00/parosci.nc INFO 2025-06-26 14:48:34,237 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:48:34,237 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.125.00/parosci.nc INFO 2025-06-26 14:48:34,241 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1241562645.4, sensor_off_time = 1241633375.3 INFO 2025-06-26 14:48:34,241 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 70729 seconds. Expecting to read 141458 L frames from the lopc.bin file. INFO 2025-06-26 14:48:34,241 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 141458 records from the lopc.bin file. INFO 2025-06-26 14:48:35,099 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-05-05 22:30:45 Z and endTime = 2009-05-06 18:09:35 Z with 141458 records expected to be read from lopc.bin INFO 2025-06-26 14:48:35,100 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.125.00/lopc.bin INFO 2025-06-26 14:48:35,100 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.125.00/lopc.nc INFO 2025-06-26 14:48:35,100 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.125.00/lopc.nc INFO 2025-06-26 14:48:35,100 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.125.00 INFO 2025-06-26 14:48:35,101 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:48:35,136 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:48:35,136 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:48:35,136 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 14:48:38,241 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10082 4858 0 0 0 0 82 3.1 seconds, last L Frame: 141458 INFO 2025-06-26 14:48:41,361 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 20162 9385 0 0 0 0 162 3.1 seconds, last L Frame: 141458 INFO 2025-06-26 14:48:44,473 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 30247 13870 0 0 0 0 247 3.1 seconds, last L Frame: 141458 INFO 2025-06-26 14:48:47,516 lopcToNetCDF.py unpackLOPCbin():1013 [1] 40000 40318 17690 0 0 0 0 318 3.0 seconds, last L Frame: 141458 INFO 2025-06-26 14:48:50,482 lopcToNetCDF.py unpackLOPCbin():1013 [1] 50000 50386 21133 0 0 0 0 386 3.0 seconds, last L Frame: 141458 INFO 2025-06-26 14:48:53,470 lopcToNetCDF.py unpackLOPCbin():1013 [1] 60000 60441 24086 0 0 0 0 441 3.0 seconds, last L Frame: 141458 INFO 2025-06-26 14:48:56,707 lopcToNetCDF.py unpackLOPCbin():1013 [1] 70000 5250 29501 0 0 0 0 786 3.2 seconds, last L Frame: 141458 INFO 2025-06-26 14:49:00,340 lopcToNetCDF.py unpackLOPCbin():1013 [1] 80000 15327 37305 0 0 0 0 863 3.6 seconds, last L Frame: 141458 INFO 2025-06-26 14:49:03,711 lopcToNetCDF.py unpackLOPCbin():1013 [1] 90000 25400 44270 0 0 0 0 936 3.4 seconds, last L Frame: 141458 INFO 2025-06-26 14:49:07,138 lopcToNetCDF.py unpackLOPCbin():1013 [1] 100000 35468 51226 0 0 0 0 1004 3.4 seconds, last L Frame: 141458 INFO 2025-06-26 14:49:10,664 lopcToNetCDF.py unpackLOPCbin():1013 [1] 110000 45536 59270 0 0 0 0 1072 3.5 seconds, last L Frame: 141458 INFO 2025-06-26 14:49:14,239 lopcToNetCDF.py unpackLOPCbin():1013 [1] 120000 55610 67172 0 0 0 0 1146 3.6 seconds, last L Frame: 141458 INFO 2025-06-26 14:49:17,955 lopcToNetCDF.py unpackLOPCbin():1013 [1] 130000 403 75537 1 1 1 0 1471 3.7 seconds, last L Frame: 141458 INFO 2025-06-26 14:49:21,071 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 14:49:21,071 lopcToNetCDF.py main():2346 [1] lFrameCount = 139913, mFrameCount = 80374 INFO 2025-06-26 14:49:21,071 lopcToNetCDF.py main():2352 [1] countBeginMFrameWithoutEndOfPreviousFrame = 1, countBeginLFrameWithoutEndOfPreviousFrame = 1 INFO 2025-06-26 14:49:21,071 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.125.00/parosci.nc INFO 2025-06-26 14:49:21,071 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:49:21,071 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.125.00/parosci.nc INFO 2025-06-26 14:49:21,075 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1241562645.4, sensor_off_time = 1241633375.3 INFO 2025-06-26 14:49:21,075 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 70729 seconds. Expecting to read 141458 L frames from the lopc.bin file. INFO 2025-06-26 14:49:21,075 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 141458 records from the lopc.bin file. INFO 2025-06-26 14:49:21,075 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 141459 INFO 2025-06-26 14:49:21,087 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [ 65535 131071] INFO 2025-06-26 14:49:21,087 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 65535, i = 1 INFO 2025-06-26 14:49:21,090 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 131071, i = 2 INFO 2025-06-26 14:49:21,091 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1 2 3 ... 141463 141464 141465] INFO 2025-06-26 14:49:21,091 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 14:49:21,092 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 510 stuck values at indices: [ 65280 65281 65282 65283 65284 65285 65286 65287 65288 65289 65290 65291 65292 65293 65294 65295 65296 65297 65298 65299 65300 65301 65302 65303 65304 65305 65306 65307 65308 65309 65310 65311 65312 65313 65314 65315 65316 65317 65318 65319 65320 65321 65322 65323 65324 65325 65326 65327 65328 65329 65330 65331 65332 65333 65334 65335 65336 65337 65338 65339 65340 65341 65342 65343 65344 65345 65346 65347 65348 65349 65350 65351 65352 65353 65354 65355 65356 65357 65358 65359 65360 65361 65362 65363 65364 65365 65366 65367 65368 65369 65370 65371 65372 65373 65374 65375 65376 65377 65378 65379 65380 65381 65382 65383 65384 65385 65386 65387 65388 65389 65390 65391 65392 65393 65394 65395 65396 65397 65398 65399 65400 65401 65402 65403 65404 65405 65406 65407 65408 65409 65410 65411 65412 65413 65414 65415 65416 65417 65418 65419 65420 65421 65422 65423 65424 65425 65426 65427 65428 65429 65430 65431 65432 65433 65434 65435 65436 65437 65438 65439 65440 65441 65442 65443 65444 65445 65446 65447 65448 65449 65450 65451 65452 65453 65454 65455 65456 65457 65458 65459 65460 65461 65462 65463 65464 65465 65466 65467 65468 65469 65470 65471 65472 65473 65474 65475 65476 65477 65478 65479 65480 65481 65482 65483 65484 65485 65486 65487 65488 65489 65490 65491 65492 65493 65494 65495 65496 65497 65498 65499 65500 65501 65502 65503 65504 65505 65506 65507 65508 65509 65510 65511 65512 65513 65514 65515 65516 65517 65518 65519 65520 65521 65522 65523 65524 65525 65526 65527 65528 65529 65530 65531 65532 65533 65534 130816 130817 130818 130819 130820 130821 130822 130823 130824 130825 130826 130827 130828 130829 130830 130831 130832 130833 130834 130835 130836 130837 130838 130839 130840 130841 130842 130843 130844 130845 130846 130847 130848 130849 130850 130851 130852 130853 130854 130855 130856 130857 130858 130859 130860 130861 130862 130863 130864 130865 130866 130867 130868 130869 130870 130871 130872 130873 130874 130875 130876 130877 130878 130879 130880 130881 130882 130883 130884 130885 130886 130887 130888 130889 130890 130891 130892 130893 130894 130895 130896 130897 130898 130899 130900 130901 130902 130903 130904 130905 130906 130907 130908 130909 130910 130911 130912 130913 130914 130915 130916 130917 130918 130919 130920 130921 130922 130923 130924 130925 130926 130927 130928 130929 130930 130931 130932 130933 130934 130935 130936 130937 130938 130939 130940 130941 130942 130943 130944 130945 130946 130947 130948 130949 130950 130951 130952 130953 130954 130955 130956 130957 130958 130959 130960 130961 130962 130963 130964 130965 130966 130967 130968 130969 130970 130971 130972 130973 130974 130975 130976 130977 130978 130979 130980 130981 130982 130983 130984 130985 130986 130987 130988 130989 130990 130991 130992 130993 130994 130995 130996 130997 130998 130999 131000 131001 131002 131003 131004 131005 131006 131007 131008 131009 131010 131011 131012 131013 131014 131015 131016 131017 131018 131019 131020 131021 131022 131023 131024 131025 131026 131027 131028 131029 131030 131031 131032 131033 131034 131035 131036 131037 131038 131039 131040 131041 131042 131043 131044 131045 131046 131047 131048 131049 131050 131051 131052 131053 131054 131055 131056 131057 131058 131059 131060 131061 131062 131063 131064 131065 131066 131067 131068 131069 131070] INFO 2025-06-26 14:49:21,095 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 14:49:21,095 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 14:49:21,095 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1 2 3 ... 141463 141464 141465] INFO 2025-06-26 14:49:21,095 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1 2 3 ... 141463 141464 141465] with len(correctedSampleCountList) = 141459 INFO 2025-06-26 14:49:21,095 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-26 14:49:21,095 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 14:49:21,096 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 ... 7.07310e+04 7.07315e+04 7.07320e+04] INFO 2025-06-26 14:49:21,097 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.24156265e+09 1.24156265e+09 1.24156265e+09 ... 1.24163338e+09 1.24163338e+09 1.24163338e+09] INFO 2025-06-26 14:49:21,097 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1241562645.4 1241562645.9, ..., timestampArray[-2:] = 1241633376.9 1241633377.4] INFO 2025-06-26 14:49:21,240 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1241562645.3517957), np.float64(1241562645.8517957)], ..., timestampList[-2:] = [np.float64(1241633376.8517957), np.float64(1241633377.3517957)]] INFO 2025-06-26 14:49:21,240 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 141459) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:49:21,240 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [139880, 139901] INFO 2025-06-26 14:49:21,241 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 6662 INFO 2025-06-26 14:49:21,241 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 141459 INFO 2025-06-26 14:49:21,241 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1241562645.3517957), np.float64(1241562645.8517957)], ..., timestampList[-2:] = [np.float64(1241633376.8517957), np.float64(1241633377.3517957)]] INFO 2025-06-26 14:49:21,241 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 141459) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:49:21,243 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(139879), np.int32(139900)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 14:49:21,250 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 6662 INFO 2025-06-26 14:49:21,252 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 14:49:21,263 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 6662 INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1241562654.8517957)], ..., tsList[-2:] = [np.float64(1241632587.8517957), np.float64(1241632598.3517957)] INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2009-05-05 22:30:54 Z INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2009-05-06 17:56:38 Z INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 139913 INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:49:21,281 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:49:21,287 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2009.125.00/lopc.nc INFO 2025-06-26 14:49:21,287 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 14:49:21 2025 Elapsed processing time from start of processing = 47 seconds INFO 2025-06-26 14:49:21,291 process.py calibrate():227 [1] Calibration steps for 2009.125.00 INFO 2025-06-26 14:49:21,933 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 14:49:21,935 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:49:22,731 calibrate.py _nudge_pos():1806 [1] 103: 0.190 0.0008092 -0.0009799 11695 39.08 3.073 -4.646 2009-05-05T23:11:28.374437120 INFO 2025-06-26 14:49:23,312 calibrate.py _nudge_pos():1806 [1] 160: 0.190 0.0019775 -0.0014624 10782 35.96 8.161 -7.536 2009-05-05T23:48:22.372768000 INFO 2025-06-26 14:49:23,845 calibrate.py _nudge_pos():1806 [1] 213: 0.190 0.0027140 -0.0019589 13085 43.63 9.233 -8.320 2009-05-06T00:32:52.379859712 INFO 2025-06-26 14:49:24,344 calibrate.py _nudge_pos():1806 [1] 262: 0.200 0.0003760 -0.0007727 5876 19.59 2.848 -7.307 2009-05-06T00:53:16.376010496 INFO 2025-06-26 14:49:24,869 calibrate.py _nudge_pos():1806 [1] 314: 0.010 -0.0002370 -0.0032812 15814 52.75 -0.667 -11.527 2009-05-06T01:46:52.575685376 INFO 2025-06-26 14:49:25,416 calibrate.py _nudge_pos():1806 [1] 367: 0.010 -0.0023224 -0.0012168 12067 40.23 -8.570 -5.605 2009-05-06T02:27:58.576752896 INFO 2025-06-26 14:49:26,039 calibrate.py _nudge_pos():1806 [1] 426: 0.020 -0.0032084 0.0011517 13595 45.33 -10.509 4.708 2009-05-06T03:14:16.576446976 INFO 2025-06-26 14:49:26,626 calibrate.py _nudge_pos():1806 [1] 483: 0.020 -0.0036951 0.0017838 11388 37.96 -14.453 8.707 2009-05-06T03:53:10.576556800 INFO 2025-06-26 14:49:27,211 calibrate.py _nudge_pos():1806 [1] 538: 0.030 -0.0053299 0.0008064 14906 49.70 -15.927 3.007 2009-05-06T04:43:46.578576640 INFO 2025-06-26 14:49:27,736 calibrate.py _nudge_pos():1806 [1] 588: 0.030 -0.0030840 0.0006339 9473 31.58 -14.503 3.719 2009-05-06T05:16:10.575403776 INFO 2025-06-26 14:49:28,303 calibrate.py _nudge_pos():1806 [1] 641: 0.040 -0.0057448 0.0028411 16897 56.33 -15.147 9.346 2009-05-06T06:13:22.570295808 INFO 2025-06-26 14:49:28,862 calibrate.py _nudge_pos():1806 [1] 694: 0.040 -0.0021508 0.0012111 9368 31.23 -10.230 7.186 2009-05-06T06:45:28.578355200 INFO 2025-06-26 14:49:29,409 calibrate.py _nudge_pos():1806 [1] 745: 0.050 -0.0039244 0.0000124 16755 55.86 -10.436 0.041 2009-05-06T07:42:10.575302656 INFO 2025-06-26 14:49:29,958 calibrate.py _nudge_pos():1806 [1] 797: 0.050 -0.0017000 -0.0010492 9072 30.25 -8.350 -6.428 2009-05-06T08:13:16.577472768 INFO 2025-06-26 14:49:30,521 calibrate.py _nudge_pos():1806 [1] 850: 0.060 -0.0034291 -0.0032996 14408 48.03 -10.607 -12.730 2009-05-06T09:02:10.576480000 INFO 2025-06-26 14:49:31,172 calibrate.py _nudge_pos():1806 [1] 911: 0.060 -0.0012039 -0.0022122 8279 27.60 -6.482 -14.854 2009-05-06T09:30:46.578925568 INFO 2025-06-26 14:49:31,668 calibrate.py _nudge_pos():1806 [1] 958: 0.060 -0.0006156 -0.0029847 8262 27.55 -3.321 -20.078 2009-05-06T09:59:05.572536832 INFO 2025-06-26 14:49:32,342 calibrate.py _nudge_pos():1806 [1] 1021: 0.070 -0.0001970 -0.0050449 6433 21.45 -1.365 -43.588 2009-05-06T10:21:34.570124032 INFO 2025-06-26 14:49:32,848 calibrate.py _nudge_pos():1806 [1] 1068: 0.060 -0.0000286 -0.0000643 50 0.16 -26.017 -72.978 2009-05-06T10:22:30.576287232 INFO 2025-06-26 14:49:32,894 calibrate.py _nudge_pos():1806 [1] 1072: 0.060 -0.0003096 -0.0070369 9987 33.30 -1.382 -39.161 2009-05-06T10:55:51.579209216 INFO 2025-06-26 14:49:33,475 calibrate.py _nudge_pos():1806 [1] 1126: 0.070 -0.0009023 -0.0029351 13718 45.73 -2.931 -11.893 2009-05-06T11:42:28.577601792 INFO 2025-06-26 14:49:34,120 calibrate.py _nudge_pos():1806 [1] 1186: 0.070 -0.0008620 0.0004598 13742 45.81 -2.795 1.860 2009-05-06T12:29:16.575240704 INFO 2025-06-26 14:49:34,788 calibrate.py _nudge_pos():1806 [1] 1248: 0.080 -0.0043913 0.0016946 13491 44.98 -14.501 6.981 2009-05-06T13:15:16.576167680 INFO 2025-06-26 14:49:35,532 calibrate.py _nudge_pos():1806 [1] 1316: 0.090 -0.0056407 0.0024814 14390 47.98 -17.461 9.583 2009-05-06T14:04:22.574352896 INFO 2025-06-26 14:49:36,214 calibrate.py _nudge_pos():1806 [1] 1378: 0.090 -0.0037688 0.0028174 14480 48.28 -11.593 10.813 2009-05-06T14:53:40.571716352 INFO 2025-06-26 14:49:36,859 calibrate.py _nudge_pos():1806 [1] 1435: 0.090 -0.0012344 -0.0001487 14177 47.26 -3.878 -0.583 2009-05-06T15:41:52.573600512 INFO 2025-06-26 14:49:37,450 calibrate.py _nudge_pos():1806 [1] 1488: 0.090 -0.0001666 -0.0000239 13987 46.63 -0.530 -0.095 2009-05-06T16:29:22.578362112 INFO 2025-06-26 14:49:38,279 calibrate.py _nudge_pos():1806 [1] 1563: 0.100 0.0012854 0.0006477 13036 43.46 4.391 2.761 2009-05-06T17:14:04.574632704 INFO 2025-06-26 14:49:38,935 calibrate.py _nudge_pos():1806 [1] 1622: 0.100 -0.0002034 0.0009728 13058 43.53 -0.694 4.141 2009-05-06T17:58:34.571725056 INFO 2025-06-26 14:49:46,274 calibrate.py _nudge_pos():1862 [1] 2251: - - - 3 0.01 - - INFO 2025-06-26 14:49:46,274 calibrate.py _nudge_pos():1868 [1] Points in final series = 353283 WARNING 2025-06-26 14:49:46,735 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:50:21,618 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 282697 INFO 2025-06-26 14:50:23,814 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:50:43,841 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 51 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:50:45,928 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 51 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:50:45,932 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.125.00/ctd1.nc INFO 2025-06-26 14:50:45,933 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:50:45,934 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 14:50:45,934 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:51:01,420 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:51:03,488 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:51:03,492 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.125.00/ctd2.nc INFO 2025-06-26 14:51:03,494 calibrate.py _range_qc_combined_nc():898 [1] Setting 153 ctd2_salinity values to NaN INFO 2025-06-26 14:51:03,494 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 14:51:03,494 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:51:05,941 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:51:09,181 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4205709 4229940 4234560] INFO 2025-06-26 14:51:09,829 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:51:09,837 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 14:51:09,848 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.125.00 INFO 2025-06-26 14:51:09,906 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_cal.nc INFO 2025-06-26 14:51:31,914 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_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, 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 14:51:31,926 process.py align():251 [1] Alignment steps for 2009.125.00 INFO 2025-06-26 14:51:31,984 align.py process_cal():139 [1] Processing dorado_2009.125.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.125.00 INFO 2025-06-26 14:51:32,088 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:51:32,098 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:51:32,324 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:51:32,337 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:51:32,557 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:51:32,573 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:51:32,702 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:51:32,702 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:51:32,786 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:51:32,798 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:51:33,006 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:33,017 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:33,202 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:33,213 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:33,404 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:33,415 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:33,611 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:33,621 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:33,817 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:33,827 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:34,020 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:34,031 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:34,218 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:34,228 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:34,415 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:34,425 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:34,622 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:34,632 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:34,818 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:34,830 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:35,021 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:35,031 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:35,220 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:35,230 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:35,421 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:35,430 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:35,618 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:35,629 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:35,818 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:35,829 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:36,018 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:36,028 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:36,218 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:36,229 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:36,416 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:36,429 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:36,620 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:36,630 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:36,818 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.125.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:51:36,828 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:51:37,059 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.72 INFO 2025-06-26 14:51:37,197 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.72 INFO 2025-06-26 14:51:37,339 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.72 INFO 2025-06-26 14:51:37,485 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:51:37,644 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:51:37,770 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:51:37,895 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:51:38,032 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:51:38,154 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:51:38,283 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 14:51:38,324 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_align.nc INFO 2025-06-26 14:51:38,483 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_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, 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 14:51:38,486 process.py resample():273 [1] Resampling steps for 2009.125.00 INFO 2025-06-26 14:51:38,487 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:51:38,523 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_align.nc mission netCDF file INFO 2025-06-26 14:51:38,532 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_align.nc mission netCDF file INFO 2025-06-26 14:51:38,534 resample.py get_mission_start_end():1145 [1] navigation: 2009-05-05T22:31:14.329810432 to 2009-05-06T18:09:35.176470784 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 14:51:38,537 resample.py get_mission_start_end():1145 [1] hs2 : 2009-05-05T22:30:50.941412608 to 2009-05-06T18:09:35.246466048 (0 days 00:00:00.059995648 before mission_end) INFO 2025-06-26 14:51:38,540 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-05-05T22:31:36.768273408 to 2009-05-06T18:09:35.306461696 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:51:38,542 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-05-05T22:31:12.699922176 to 2009-05-06T18:09:35.116474880 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 14:51:38,544 resample.py get_mission_start_end():1145 [1] isus : 2009-05-05T22:31:43.237830144 to 2009-05-06T18:09:35.186470144 (0 days 00:00:00.119991552 before mission_end) INFO 2025-06-26 14:51:38,546 resample.py get_mission_start_end():1145 [1] biolume : 2009-05-05T22:30:42.191977728 to 2009-05-06T18:09:34.376491264 (0 days 00:00:00.929970432 before mission_end) INFO 2025-06-26 14:51:38,547 resample.py get_mission_start_end():1145 [1] lopc : 2009-05-05T22:30:54.851795712 to 2009-05-06T17:56:38.351795712 (0 days 00:12:56.954665984 before mission_end) WARNING 2025-06-26 14:51:38,548 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 00:12:56.954665984 INFO 2025-06-26 14:51:38,549 resample.py get_mission_start_end():1145 [1] tailcone : 2009-05-05T22:30:48.341590784 to 2009-05-06T18:09:34.646507008 (0 days 00:00:00.659954688 before mission_end) INFO 2025-06-26 14:51:38,550 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_align.nc mission netCDF file INFO 2025-06-26 14:51:38,550 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,250 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,365 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,475 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,586 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,682 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,776 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,868 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:39,960 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,056 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,142 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,230 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,315 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,402 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,489 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,579 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,666 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,758 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,853 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:40,951 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,043 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,134 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,225 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,260 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,289 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,315 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,349 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,366 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,366 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 00:12:56.954665984 of NaNs to the end of mission INFO 2025-06-26 14:51:41,385 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,385 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 00:12:56.954665984 of NaNs to the end of mission INFO 2025-06-26 14:51:41,403 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,403 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 00:12:56.954665984 of NaNs to the end of mission INFO 2025-06-26 14:51:41,420 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,421 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 00:12:56.954665984 of NaNs to the end of mission INFO 2025-06-26 14:51:41,439 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,439 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 00:12:56.954665984 of NaNs to the end of mission INFO 2025-06-26 14:51:41,474 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:51:41,979 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_1S.nc INFO 2025-06-26 14:51:45,112 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 14:51:46,389 create_products.py gulper_odv():522 [1] Wrote 1 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.125.00/dorado_2009.125.00_1S_Gulper.txt INFO 2025-06-26 14:51:46,389 process.py archive():337 [1] Archiving steps for 2009.125.00 INFO 2025-06-26 14:51:46,389 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00, BASE_PATH = /data/auv_data INFO 2025-06-26 14:51:46,391 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 14:51:46,392 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.125.00_1S.nc INFO 2025-06-26 14:51:46,449 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:51:46,450 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.125.00_cal.nc INFO 2025-06-26 14:51:46,684 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:51:46,685 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.125.00_align.nc INFO 2025-06-26 14:51:46,918 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:51:46,983 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,054 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,059 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,124 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,343 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,353 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,434 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,450 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,627 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,825 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009125/2009.125.00 done. INFO 2025-06-26 14:51:47,825 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:51:47,827 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.125.00_1S_Gulper.txt INFO 2025-06-26 14:51:47,832 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.125.00/dorado_2009.125.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 14:51:47,832 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.125.00/dorado_2009.125.00_processing.log /Volumes/AUVCTD/surveys/2009/netcdf