INFO 2025-06-26 14:58:24,242 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 14:58:24,242 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Ryan - around ESP - ctdToUse = ctd2 INFO 2025-06-26 14:58:24,242 process.py process_mission():449 [1] Processing AUVCTD mission 2009.154.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:58:24,242 process.py download_process():165 [1] Download and processing steps for 2009.154.00 INFO 2025-06-26 14:58:24,242 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009154/2009.154.00 INFO 2025-06-26 14:58:24,242 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009154/2009.154.00 to /data/auv_data/dorado/missionlogs/2009.154.00 INFO 2025-06-26 14:58:31,490 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.154.00 INFO 2025-06-26 14:58:31,490 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/ctdDriver.log (21142132 bytes) INFO 2025-06-26 14:58:32,951 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.154.00/ctdDriver.log: [ 17756 28136 28366 31978 46200 53312 54748 60013 60424 61934 65637 74646 80354 88784 88869 90337 93550 95919 100503 108923 110483 115635 117312 121661 132708 133130 140351 144594 148129 162130 169341 171343 174204 175303 177975 179581 188426 190418 198432 202647 215397 215619 220553 238203 238861] INFO 2025-06-26 14:58:33,013 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/ctdDriver2.log (21150925 bytes) INFO 2025-06-26 14:58:34,507 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.154.00/ctdDriver2.log: [ 7739 20146 23069 30192 39035 41893 48605 49492 55318 57672 60112 65521 65619 76654 77253 80735 95731 100433 102310 104901 107874 110301 123266 127538 131634 137297 140559 140731 152969 156014 159197 160809 162230 163645 170415 174304 180876 209859 215497 223221 238303] INFO 2025-06-26 14:58:34,580 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/gps.log (117068 bytes) INFO 2025-06-26 14:58:34,601 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/hydroscatlog.log (20186146 bytes) INFO 2025-06-26 14:58:36,619 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.154.00/hydroscatlog.log: [ 15380 30545 30982 35211 35245 38243 40240 58292 60578 70248 71298 73282 80778 88270 100635 117435 120670 122769 127557 135888 142598 148911 153810 160808 162229 172733 175395 176144 179671 180864 190860 194421 194468 197176 200888 202724 202983 208193 211060 224048 231148] INFO 2025-06-26 14:58:36,688 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/navigation.log (70874230 bytes) INFO 2025-06-26 14:58:41,817 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/isuslog.log (1396821 bytes) INFO 2025-06-26 14:58:41,954 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/parosci.log (24615638 bytes) INFO 2025-06-26 14:58:44,058 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/tailCone.log (2915467 bytes) INFO 2025-06-26 14:58:44,421 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/biolume.log (16354956 bytes) INFO 2025-06-26 14:58:45,993 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:58:46,846 logs2netcdfs.py download_process_logs():807 [1] Time to process: 15.36 seconds INFO 2025-06-26 14:58:46,846 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.154.00/lopc.bin (67589118 bytes) INFO 2025-06-26 14:58:46,846 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:58:46 2025 INFO 2025-06-26 14:58:46,846 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.154.00/parosci.nc INFO 2025-06-26 14:58:46,846 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:58:46,846 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.154.00/parosci.nc INFO 2025-06-26 14:58:46,850 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1244067355.9, sensor_off_time = 1244127466.5 INFO 2025-06-26 14:58:46,850 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 60110 seconds. Expecting to read 120220 L frames from the lopc.bin file. INFO 2025-06-26 14:58:46,850 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 120220 records from the lopc.bin file. INFO 2025-06-26 14:58:47,561 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-06-03 22:15:55 Z and endTime = 2009-06-04 14:57:46 Z with 120220 records expected to be read from lopc.bin INFO 2025-06-26 14:58:47,561 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.154.00/lopc.bin INFO 2025-06-26 14:58:47,561 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.154.00/lopc.nc INFO 2025-06-26 14:58:47,561 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.154.00/lopc.nc INFO 2025-06-26 14:58:47,562 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.154.00 INFO 2025-06-26 14:58:47,562 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:58:47,610 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:58:47,610 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:58:47,610 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 14:58:54,113 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10079 16449 0 0 0 0 79 6.6 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:00,981 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 20158 33942 0 0 0 0 158 6.9 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:08,060 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 30233 51847 0 0 0 0 233 7.1 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:17,096 lopcToNetCDF.py unpackLOPCbin():1013 [1] 40000 40315 75350 0 0 0 0 315 9.0 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:26,425 lopcToNetCDF.py unpackLOPCbin():1013 [1] 50000 50384 99910 0 0 0 0 384 9.3 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:34,719 lopcToNetCDF.py unpackLOPCbin():1013 [1] 60000 60463 121001 0 0 0 0 463 8.3 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:44,999 lopcToNetCDF.py unpackLOPCbin():1013 [1] 70000 5274 147488 0 0 0 0 810 10.3 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:52,401 lopcToNetCDF.py unpackLOPCbin():1013 [1] 80000 15357 166305 0 0 0 0 893 7.4 seconds, last L Frame: 120220 INFO 2025-06-26 14:59:59,122 lopcToNetCDF.py unpackLOPCbin():1013 [1] 90000 25433 183311 0 0 0 0 969 6.7 seconds, last L Frame: 120220 INFO 2025-06-26 15:00:06,459 lopcToNetCDF.py unpackLOPCbin():1013 [1] 100000 35522 201488 0 0 0 0 1058 7.3 seconds, last L Frame: 120220 INFO 2025-06-26 15:00:12,955 lopcToNetCDF.py unpackLOPCbin():1013 [1] 110000 45597 215857 0 0 0 0 1133 6.5 seconds, last L Frame: 120220 INFO 2025-06-26 15:00:19,564 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 15:00:19,564 lopcToNetCDF.py main():2346 [1] lFrameCount = 119016, mFrameCount = 229794 INFO 2025-06-26 15:00:19,564 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.154.00/parosci.nc INFO 2025-06-26 15:00:19,564 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:00:19,564 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.154.00/parosci.nc INFO 2025-06-26 15:00:19,568 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1244067355.9, sensor_off_time = 1244127466.5 INFO 2025-06-26 15:00:19,568 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 60110 seconds. Expecting to read 120220 L frames from the lopc.bin file. INFO 2025-06-26 15:00:19,568 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 120220 records from the lopc.bin file. INFO 2025-06-26 15:00:19,568 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 120222 INFO 2025-06-26 15:00:19,578 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [65535] INFO 2025-06-26 15:00:19,579 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 65535, i = 1 INFO 2025-06-26 15:00:19,581 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1 2 3 ... 120221 120222 120223] INFO 2025-06-26 15:00:19,581 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 15:00:19,582 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 255 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] INFO 2025-06-26 15:00:19,583 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 15:00:19,584 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 15:00:19,584 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1 2 3 ... 120221 120222 120223] INFO 2025-06-26 15:00:19,584 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1 2 3 ... 120221 120222 120223] with len(correctedSampleCountList) = 120222 INFO 2025-06-26 15:00:19,584 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-26 15:00:19,584 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 15:00:19,584 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 ... 6.01100e+04 6.01105e+04 6.01110e+04] INFO 2025-06-26 15:00:19,585 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.24406736e+09 1.24406736e+09 1.24406736e+09 ... 1.24412747e+09 1.24412747e+09 1.24412747e+09] INFO 2025-06-26 15:00:19,585 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1244067355.9 1244067356.4, ..., timestampArray[-2:] = 1244127466.4 1244127466.9] INFO 2025-06-26 15:00:19,707 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1244067355.8611243), np.float64(1244067356.3611243)], ..., timestampList[-2:] = [np.float64(1244127466.3611243), np.float64(1244127466.8611243)]] INFO 2025-06-26 15:00:19,707 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 120222) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:00:19,708 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [118985, 119006] INFO 2025-06-26 15:00:19,708 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 5667 INFO 2025-06-26 15:00:19,708 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 120222 INFO 2025-06-26 15:00:19,708 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1244067355.8611243), np.float64(1244067356.3611243)], ..., timestampList[-2:] = [np.float64(1244127466.3611243), np.float64(1244127466.8611243)]] INFO 2025-06-26 15:00:19,708 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 120222) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:00:19,710 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(118984), np.int32(119005)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 15:00:19,716 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 5667 INFO 2025-06-26 15:00:19,717 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 15:00:19,726 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 15:00:19,743 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 5667 INFO 2025-06-26 15:00:19,743 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1244067365.3611243)], ..., tsList[-2:] = [np.float64(1244126848.3611243), np.float64(1244126858.8611243)] INFO 2025-06-26 15:00:19,743 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2009-06-03 22:16:05 Z INFO 2025-06-26 15:00:19,743 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2009-06-04 14:47:38 Z INFO 2025-06-26 15:00:19,743 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 119016 INFO 2025-06-26 15:00:19,743 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 15:00:19,743 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:00:19,744 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:00:19,748 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2009.154.00/lopc.nc INFO 2025-06-26 15:00:19,748 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 15:00:19 2025 Elapsed processing time from start of processing = 92 seconds INFO 2025-06-26 15:00:19,752 process.py calibrate():227 [1] Calibration steps for 2009.154.00 INFO 2025-06-26 15:00:20,348 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 15:00:20,350 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:00:21,229 calibrate.py _nudge_pos():1806 [1] 113: 0.140 0.0000035 -0.0002484 2515 8.38 0.061 -5.492 2009-06-03T22:26:10.299032320 INFO 2025-06-26 15:00:21,632 calibrate.py _nudge_pos():1806 [1] 153: 0.140 0.0001414 -0.0010670 10631 35.45 0.591 -5.578 2009-06-03T23:02:16.300651008 INFO 2025-06-26 15:00:21,996 calibrate.py _nudge_pos():1806 [1] 189: 0.140 0.0002071 -0.0007798 9993 33.31 0.922 -4.338 2009-06-03T23:36:10.301312512 INFO 2025-06-26 15:00:22,519 calibrate.py _nudge_pos():1806 [1] 241: 0.140 0.0002243 -0.0009485 10584 35.28 0.943 -4.982 2009-06-04T00:12:18.302794240 INFO 2025-06-26 15:00:23,058 calibrate.py _nudge_pos():1806 [1] 293: 0.150 0.0000731 -0.0006823 10052 33.51 0.324 -3.773 2009-06-04T00:46:40.301537536 INFO 2025-06-26 15:00:23,447 calibrate.py _nudge_pos():1806 [1] 329: 0.150 0.0000697 -0.0010027 8431 28.11 0.368 -6.609 2009-06-04T01:15:22.303572480 INFO 2025-06-26 15:00:23,785 calibrate.py _nudge_pos():1806 [1] 362: 0.150 0.0020019 0.0017519 10697 35.66 8.326 9.103 2009-06-04T01:51:34.304780032 INFO 2025-06-26 15:00:24,001 calibrate.py _nudge_pos():1806 [1] 383: 0.160 0.0002402 -0.0011724 11110 37.05 0.962 -5.864 2009-06-04T02:28:57.301124352 INFO 2025-06-26 15:00:24,320 calibrate.py _nudge_pos():1806 [1] 413: 0.160 0.0001380 -0.0010343 10718 35.73 0.573 -5.364 2009-06-04T03:05:10.302263552 INFO 2025-06-26 15:00:24,544 calibrate.py _nudge_pos():1806 [1] 434: 0.160 0.0000796 -0.0009967 9887 32.96 0.358 -5.603 2009-06-04T03:38:28.305391104 INFO 2025-06-26 15:00:24,894 calibrate.py _nudge_pos():1806 [1] 467: 0.170 0.0002198 -0.0009328 10997 36.66 0.889 -4.714 2009-06-04T04:15:40.302488576 INFO 2025-06-26 15:00:25,142 calibrate.py _nudge_pos():1806 [1] 490: 0.170 -0.0000136 -0.0000171 15 0.05 -43.129 -68.060 2009-06-04T04:16:05.300776192 INFO 2025-06-26 15:00:25,174 calibrate.py _nudge_pos():1806 [1] 493: 0.170 -0.0000001 -0.0009324 7604 25.35 -0.001 -6.816 2009-06-04T04:41:28.306443264 INFO 2025-06-26 15:00:25,571 calibrate.py _nudge_pos():1806 [1] 530: 0.180 0.0015975 0.0013924 11666 38.90 6.092 6.633 2009-06-04T05:20:58.304087040 INFO 2025-06-26 15:00:25,897 calibrate.py _nudge_pos():1806 [1] 560: 0.180 -0.0000074 0.0000343 20 0.06 -17.368 100.496 2009-06-04T05:21:31.301826816 INFO 2025-06-26 15:00:25,960 calibrate.py _nudge_pos():1806 [1] 566: 0.180 0.0001808 -0.0011174 9678 32.26 0.831 -6.418 2009-06-04T05:53:52.308858624 INFO 2025-06-26 15:00:26,050 calibrate.py _nudge_pos():1806 [1] 574: 0.180 -0.0002727 -0.0017026 11716 39.06 -1.036 -8.076 2009-06-04T06:33:03.307804160 INFO 2025-06-26 15:00:26,446 calibrate.py _nudge_pos():1806 [1] 610: 0.190 0.0001200 -0.0008893 9038 30.13 0.591 -5.469 2009-06-04T07:03:46.301550336 INFO 2025-06-26 15:00:26,726 calibrate.py _nudge_pos():1806 [1] 636: 0.180 -0.0000953 -0.0007483 10433 34.78 -0.406 -3.987 2009-06-04T07:38:58.306867968 INFO 2025-06-26 15:00:27,153 calibrate.py _nudge_pos():1806 [1] 675: 0.190 0.0000948 -0.0010284 7815 26.06 0.539 -7.312 2009-06-04T08:05:40.307123712 INFO 2025-06-26 15:00:27,458 calibrate.py _nudge_pos():1806 [1] 702: 0.200 0.0017499 0.0016484 11357 37.86 6.855 8.067 2009-06-04T08:43:58.299700224 INFO 2025-06-26 15:00:27,851 calibrate.py _nudge_pos():1806 [1] 738: 0.010 0.0003207 -0.0013456 10354 34.52 1.378 -7.224 2009-06-04T09:19:04.505415424 INFO 2025-06-26 15:00:28,275 calibrate.py _nudge_pos():1806 [1] 777: 0.010 0.0001190 -0.0007501 9617 32.06 0.551 -4.335 2009-06-04T09:51:46.501009408 INFO 2025-06-26 15:00:28,474 calibrate.py _nudge_pos():1806 [1] 795: 0.010 0.0001983 -0.0009915 10141 33.81 0.870 -5.434 2009-06-04T10:25:52.500848896 INFO 2025-06-26 15:00:28,777 calibrate.py _nudge_pos():1806 [1] 822: 0.010 0.0000921 -0.0006338 9676 32.26 0.423 -3.640 2009-06-04T10:58:34.506442240 INFO 2025-06-26 15:00:29,101 calibrate.py _nudge_pos():1806 [1] 851: 0.010 0.0000629 -0.0009692 7809 26.03 0.359 -6.899 2009-06-04T11:25:04.507519744 INFO 2025-06-26 15:00:29,392 calibrate.py _nudge_pos():1806 [1] 877: 0.010 0.0019932 0.0018162 10913 36.38 8.127 9.251 2009-06-04T12:01:52.506261248 INFO 2025-06-26 15:00:29,725 calibrate.py _nudge_pos():1806 [1] 907: 0.020 0.0003024 -0.0012961 8822 29.41 1.525 -8.165 2009-06-04T12:31:46.503364352 INFO 2025-06-26 15:00:30,013 calibrate.py _nudge_pos():1806 [1] 932: 0.030 0.0000950 0.0000278 2910 9.70 1.453 0.531 2009-06-04T12:41:52.501850624 INFO 2025-06-26 15:00:30,311 calibrate.py _nudge_pos():1806 [1] 959: 0.030 0.0000304 -0.0008387 9287 30.96 0.145 -5.019 2009-06-04T13:13:16.502787584 INFO 2025-06-26 15:00:30,583 calibrate.py _nudge_pos():1806 [1] 983: 0.030 0.0000467 -0.0004812 4142 13.81 0.502 -6.455 2009-06-04T13:27:28.504421376 INFO 2025-06-26 15:00:30,987 calibrate.py _nudge_pos():1806 [1] 1017: 0.030 0.0001097 -0.0004430 5983 19.95 0.816 -4.115 2009-06-04T13:47:58.500161024 INFO 2025-06-26 15:00:31,346 calibrate.py _nudge_pos():1806 [1] 1049: 0.030 0.0000615 -0.0008250 9593 31.98 0.285 -4.780 2009-06-04T14:20:28.506576384 INFO 2025-06-26 15:00:31,692 calibrate.py _nudge_pos():1806 [1] 1079: 0.030 0.0000952 -0.0010135 7955 26.51 0.533 -7.083 2009-06-04T14:47:28.505598720 INFO 2025-06-26 15:00:32,048 calibrate.py _nudge_pos():1806 [1] 1111: 0.040 0.0000207 -0.0000217 270 0.90 3.430 -4.493 2009-06-04T14:48:53.499776256 INFO 2025-06-26 15:00:32,094 calibrate.py _nudge_pos():1806 [1] 1115: 0.030 0.0000010 0.0000052 159 0.53 0.274 1.820 2009-06-04T14:49:28.507378176 INFO 2025-06-26 15:00:37,899 calibrate.py _nudge_pos():1862 [1] 1580: - - - 0 0.00 - - INFO 2025-06-26 15:00:37,899 calibrate.py _nudge_pos():1868 [1] Points in final series = 300245 INFO 2025-06-26 15:00:38,304 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=50) for self.args.mission=2009.154.00 INFO 2025-06-26 15:00:38,312 calibrate.py _depth_process():2175 [1] Setting 4 depths values to NaN WARNING 2025-06-26 15:00:38,321 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:01:11,645 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:01:29,495 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 50 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:01:31,311 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 50 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:01:31,314 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.154.00/ctd1.nc INFO 2025-06-26 15:01:31,316 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 15:01:31,316 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 15:01:31,316 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:01:44,771 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:01:46,643 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:01:46,647 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.154.00/ctd2.nc INFO 2025-06-26 15:01:46,648 calibrate.py _range_qc_combined_nc():898 [1] Setting 90 ctd2_salinity values to NaN INFO 2025-06-26 15:01:46,649 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 15:01:46,649 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 15:01:46,739 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 15:01:49,469 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 840 6960 7440 7441 7442 7443 24420 24421 24422 24423 24424 24425 24426 32580 32581 32582 32583 32584 32585 48780 48781 48782 102120 102121 102122 102123 115320 117300 117720 117721 117722 117723 117724 117725 129600 129601 129602 129603 129604 129605 129606 129607 129608 129609 129610 129611 129612 174720 174721 174722 174723 174724 174725 174726 174727 174728 174729 189780 189781 189782 189783 189784 189785 189786 189787 312720 312721 312722 312723 312724 312725 312726 312727 312728 312729 312730 312731 312732 312733 312734 312735 312736 312737 312738 425220 425221 425222 425223 425224 425225 425226 436800 436801 488400 587220 587221 587222 587223 587224 587225 587226 587227 587228 587229 587230 587231 587232 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[1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 15:01:50,004 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 15:01:50,016 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.154.00 INFO 2025-06-26 15:01:50,081 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_cal.nc INFO 2025-06-26 15:02:09,246 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 15:02:09,260 process.py align():251 [1] Alignment steps for 2009.154.00 INFO 2025-06-26 15:02:09,312 align.py process_cal():139 [1] Processing dorado_2009.154.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.154.00 INFO 2025-06-26 15:02:09,394 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:02:09,402 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:02:09,598 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:02:09,609 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:02:09,805 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:02:09,819 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:02:09,931 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:02:09,931 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:02:10,009 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:02:10,020 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:02:10,205 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:10,216 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:10,382 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:10,392 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:10,559 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:10,569 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:10,746 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:10,756 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:10,921 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:10,931 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:11,097 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:11,106 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:11,272 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:11,282 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:11,444 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:11,453 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:11,618 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:11,628 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:11,794 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:11,807 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:11,969 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:11,979 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:12,164 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:12,173 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:12,340 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:12,348 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:12,512 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:12,522 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:12,699 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:12,710 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:12,876 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:12,887 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:13,056 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:13,066 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:13,232 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:13,244 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:13,409 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:13,419 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:13,586 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.154.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:02:13,596 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:02:13,799 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:02:13,920 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:02:14,047 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:02:14,174 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 15:02:14,304 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:02:14,412 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:02:14,521 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:02:14,629 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:02:14,737 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:02:14,848 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 15:02:14,885 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_align.nc INFO 2025-06-26 15:02:15,111 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 15:02:15,114 process.py resample():273 [1] Resampling steps for 2009.154.00 INFO 2025-06-26 15:02:15,115 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:02:15,151 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_align.nc mission netCDF file INFO 2025-06-26 15:02:15,160 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_align.nc mission netCDF file INFO 2025-06-26 15:02:15,162 resample.py get_mission_start_end():1145 [1] navigation: 2009-06-03T22:16:28.638878720 to 2009-06-04T14:57:46.503263232 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:02:15,165 resample.py get_mission_start_end():1145 [1] hs2 : 2009-06-03T22:16:01.220756992 to 2009-06-04T14:57:46.433267712 (0 days 00:00:00.069995520 before mission_end) INFO 2025-06-26 15:02:15,167 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-06-03T22:16:46.627646464 to 2009-06-04T14:57:46.363272704 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 15:02:15,170 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-06-03T22:16:22.029331456 to 2009-06-04T14:57:46.433267712 (0 days 00:00:00.069995520 before mission_end) INFO 2025-06-26 15:02:15,172 resample.py get_mission_start_end():1145 [1] isus : 2009-06-03T22:17:17.535529216 to 2009-06-04T14:57:45.423337216 (0 days 00:00:01.079926016 before mission_end) INFO 2025-06-26 15:02:15,173 resample.py get_mission_start_end():1145 [1] biolume : 2009-06-03T22:15:55.171137280 to 2009-06-04T14:57:45.553293824 (0 days 00:00:00.949969408 before mission_end) INFO 2025-06-26 15:02:15,175 resample.py get_mission_start_end():1145 [1] lopc : 2009-06-03T22:16:05.361124352 to 2009-06-04T14:47:38.861124352 (0 days 00:10:07.642138880 before mission_end) WARNING 2025-06-26 15:02:15,175 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 00:10:07.642138880 INFO 2025-06-26 15:02:15,176 resample.py get_mission_start_end():1145 [1] tailcone : 2009-06-03T22:16:00.440810496 to 2009-06-04T14:57:46.143287808 (0 days 00:00:00.359975424 before mission_end) INFO 2025-06-26 15:02:15,177 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_align.nc mission netCDF file INFO 2025-06-26 15:02:15,178 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:15,816 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:15,916 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,017 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,118 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,202 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,286 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,370 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,450 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,526 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,603 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,680 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,759 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,838 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,916 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:16,992 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,071 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,155 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,242 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,332 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,416 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,500 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,583 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,614 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,641 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,667 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,699 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,717 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,717 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 00:10:07.642138880 of NaNs to the end of mission INFO 2025-06-26 15:02:17,736 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,737 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 00:10:07.642138880 of NaNs to the end of mission INFO 2025-06-26 15:02:17,754 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,754 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 00:10:07.642138880 of NaNs to the end of mission INFO 2025-06-26 15:02:17,771 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,771 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 00:10:07.642138880 of NaNs to the end of mission INFO 2025-06-26 15:02:17,787 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:17,787 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 00:10:07.642138880 of NaNs to the end of mission INFO 2025-06-26 15:02:17,818 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:02:18,275 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_1S.nc INFO 2025-06-26 15:02:21,330 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 15:02:27,074 create_products.py gulper_odv():522 [1] Wrote 5 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.154.00/dorado_2009.154.00_1S_Gulper.txt INFO 2025-06-26 15:02:27,074 process.py archive():337 [1] Archiving steps for 2009.154.00 INFO 2025-06-26 15:02:27,074 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00, BASE_PATH = /data/auv_data INFO 2025-06-26 15:02:27,076 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:02:27,076 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.154.00_1S.nc INFO 2025-06-26 15:02:27,127 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:02:27,128 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.154.00_cal.nc INFO 2025-06-26 15:02:27,339 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:02:27,340 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.154.00_align.nc INFO 2025-06-26 15:02:27,529 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:02:27,587 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:27,650 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:27,655 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:27,710 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:27,877 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:27,886 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:27,952 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:27,967 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:28,132 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:28,317 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009154/2009.154.00 done. INFO 2025-06-26 15:02:28,318 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:02:28,320 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.154.00_1S_Gulper.txt INFO 2025-06-26 15:02:28,325 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.154.00/dorado_2009.154.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 15:02:28,325 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.154.00/dorado_2009.154.00_processing.log /Volumes/AUVCTD/surveys/2009/netcdf