INFO 2025-06-26 13:59:20,585 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 13:59:20,585 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Autonomy TREX mission - ctdToUse = ctd1 INFO 2025-06-26 13:59:20,585 process.py process_mission():449 [1] Processing AUVCTD mission 2008.140.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:59:20,585 process.py download_process():165 [1] Download and processing steps for 2008.140.00 INFO 2025-06-26 13:59:20,585 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008140/2008.140.00 INFO 2025-06-26 13:59:20,585 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008140/2008.140.00 to /data/auv_data/dorado/missionlogs/2008.140.00 INFO 2025-06-26 13:59:28,031 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.140.00 INFO 2025-06-26 13:59:28,032 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/ctdDriver.log (26366604 bytes) INFO 2025-06-26 13:59:29,952 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.140.00/ctdDriver.log: [ 4599 22344 73711] INFO 2025-06-26 13:59:30,038 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/ctdDriver2.log (26376013 bytes) INFO 2025-06-26 13:59:31,940 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.140.00/ctdDriver2.log: [11067 30647 31745 54621 71313] INFO 2025-06-26 13:59:32,029 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/gps.log (242492 bytes) INFO 2025-06-26 13:59:32,064 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/hydroscatlog.log (17988434 bytes) INFO 2025-06-26 13:59:34,162 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.140.00/hydroscatlog.log: [ 2188 2189 27516] INFO 2025-06-26 13:59:34,216 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/navigation.log (88452926 bytes) INFO 2025-06-26 13:59:40,670 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/isuslog.log (1865717 bytes) INFO 2025-06-26 13:59:40,847 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.140.00/isuslog.log: [1 2 3 4 5 6 7 8 9] INFO 2025-06-26 13:59:40,853 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/parosci.log (31080278 bytes) INFO 2025-06-26 13:59:43,481 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/tailCone.log (3640843 bytes) INFO 2025-06-26 13:59:43,931 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/biolume.log (20402860 bytes) INFO 2025-06-26 13:59:45,900 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:59:47,019 logs2netcdfs.py download_process_logs():807 [1] Time to process: 18.99 seconds INFO 2025-06-26 13:59:47,020 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2008.140.00/lopc.bin (52905846 bytes) INFO 2025-06-26 13:59:47,020 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 13:59:47 2025 INFO 2025-06-26 13:59:47,020 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.140.00/parosci.nc INFO 2025-06-26 13:59:47,020 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 13:59:47,020 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.140.00/parosci.nc INFO 2025-06-26 13:59:47,024 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1211232263.6, sensor_off_time = 1211307247.9 INFO 2025-06-26 13:59:47,024 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 74984 seconds. Expecting to read 149968 L frames from the lopc.bin file. INFO 2025-06-26 13:59:47,024 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 149968 records from the lopc.bin file. INFO 2025-06-26 13:59:47,921 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2008-05-19 21:24:23 Z and endTime = 2008-05-20 18:14:07 Z with 149968 records expected to be read from lopc.bin INFO 2025-06-26 13:59:47,922 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2008.140.00/lopc.bin INFO 2025-06-26 13:59:47,922 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2008.140.00/lopc.nc INFO 2025-06-26 13:59:47,923 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2008.140.00/lopc.nc INFO 2025-06-26 13:59:47,923 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2008.140.00 INFO 2025-06-26 13:59:47,923 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 13:59:48,005 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x85 in position 0: invalid start byte INFO 2025-06-26 13:59:48,005 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 13:59:48,005 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.140.00/parosci.nc INFO 2025-06-26 13:59:48,005 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 13:59:48,005 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.140.00/parosci.nc INFO 2025-06-26 13:59:48,009 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1211232263.6, sensor_off_time = 1211307247.9 INFO 2025-06-26 13:59:48,009 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 74984 seconds. Expecting to read 149968 L frames from the lopc.bin file. INFO 2025-06-26 13:59:48,009 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 149968 records from the lopc.bin file. INFO 2025-06-26 13:59:48,009 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 41 INFO 2025-06-26 13:59:48,009 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 13:59:48,010 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1 2 3 4 14 15 16 26 27 28 29 30 40 41 51 52 63 64 75 76 77 87 88 89 99 100 111 112 113 122 123 124 134 135 145 146 147 157 158 159 160] INFO 2025-06-26 13:59:48,010 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 13:59:48,010 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 13:59:48,010 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 1 10 1 1 10 1 1 1 1 10 1 10 1 11 1 11 1 1 10 1 1 10 1 11 1 1 9 1 1 10 1 10 1 1 10 1 1 1] INFO 2025-06-26 13:59:48,010 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 13:59:48,010 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1 2 3 4 14 15 16 26 27 28 29 30 40 41 51 52 63 64 75 76 77 87 88 89 99 100 111 112 113 122 123 124 134 135 145 146 147 157 158 159 160] INFO 2025-06-26 13:59:48,011 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1 2 3 4 14 15 16 26 27 28 29 30 40 41 51 52 63 64 75 76 77 87 88 89 99 100 111 112 113 122 123 124 134 135 145 146 147 157 158 159 160] with len(correctedSampleCountList) = 41 INFO 2025-06-26 13:59:48,011 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-26 13:59:48,011 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 13:59:48,011 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [ 0. 0.5 1. 1.5 6.5 7. 7.5 12.5 13. 13.5 14. 14.5 19.5 20. 25. 25.5 31. 31.5 37. 37.5 38. 43. 43.5 44. 49. 49.5 55. 55.5 56. 60.5 61. 61.5 66.5 67. 72. 72.5 73. 78. 78.5 79. 79.5] INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.21123226e+09 1.21123226e+09 1.21123226e+09 1.21123227e+09 1.21123227e+09 1.21123227e+09 1.21123227e+09 1.21123228e+09 1.21123228e+09 1.21123228e+09 1.21123228e+09 1.21123228e+09 1.21123228e+09 1.21123228e+09 1.21123229e+09 1.21123229e+09 1.21123229e+09 1.21123230e+09 1.21123230e+09 1.21123230e+09 1.21123230e+09 1.21123231e+09 1.21123231e+09 1.21123231e+09 1.21123231e+09 1.21123231e+09 1.21123232e+09 1.21123232e+09 1.21123232e+09 1.21123232e+09 1.21123232e+09 1.21123233e+09 1.21123233e+09 1.21123233e+09 1.21123234e+09 1.21123234e+09 1.21123234e+09 1.21123234e+09 1.21123234e+09 1.21123234e+09 1.21123234e+09] INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1211232263.6 1211232264.1, ..., timestampArray[-2:] = 1211232342.6 1211232343.1] INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1211232263.5731714), np.float64(1211232264.0731714)], ..., timestampList[-2:] = [np.float64(1211232342.5731714), np.float64(1211232343.0731714)]] INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 41) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20], ... lFrameCountWrittenList[-2:] = [20] INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 1 INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 41 INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1211232263.5731714), np.float64(1211232264.0731714)], ..., timestampList[-2:] = [np.float64(1211232342.5731714), np.float64(1211232343.0731714)]] INFO 2025-06-26 13:59:48,012 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 41) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 13:59:48,013 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19)] ... [np.int32(19)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 13:59:48,013 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 1 INFO 2025-06-26 13:59:48,013 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 13:59:48,013 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 1 INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1211232301.0731714)], ..., tsList[-2:] = [np.float64(1211232301.0731714)] INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2008-05-19 21:25:01 Z INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2008-05-19 21:25:01 Z INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 41 INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 13:59:48,014 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 13:59:48,018 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2008.140.00/lopc.nc INFO 2025-06-26 13:59:48,018 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 13:59:48 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 13:59:48,021 process.py calibrate():227 [1] Calibration steps for 2008.140.00 INFO 2025-06-26 13:59:48,648 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 13:59:48,650 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:59:49,423 calibrate.py _nudge_pos():1806 [1] 99: 0.120 -0.0001571 -0.0000103 2890 9.63 -2.419 -0.197 2008-05-19T21:35:36.047103744 INFO 2025-06-26 13:59:50,182 calibrate.py _nudge_pos():1806 [1] 175: 0.130 0.0000981 -0.0000065 30 0.10 150.510 -12.556 2008-05-19T21:36:57.041555200 INFO 2025-06-26 13:59:50,203 calibrate.py _nudge_pos():1806 [1] 177: 0.130 0.0001125 -0.0002629 10180 33.93 0.492 -1.436 2008-05-19T22:10:54.042011136 INFO 2025-06-26 13:59:50,679 calibrate.py _nudge_pos():1806 [1] 224: 0.120 0.0000049 -0.0000924 2740 9.13 0.080 -1.875 2008-05-19T22:20:48.051318528 INFO 2025-06-26 13:59:51,349 calibrate.py _nudge_pos():1806 [1] 290: 0.130 0.0000750 0.0003699 9365 31.21 0.357 2.196 2008-05-19T22:53:06.048556800 INFO 2025-06-26 13:59:52,059 calibrate.py _nudge_pos():1806 [1] 360: 0.120 -0.0000130 0.0000252 2385 7.95 -0.242 0.589 2008-05-19T23:02:12.051153152 INFO 2025-06-26 13:59:52,631 calibrate.py _nudge_pos():1806 [1] 417: 0.130 0.0001451 -0.0003044 10130 33.76 0.637 -1.671 2008-05-19T23:36:54.048526592 INFO 2025-06-26 13:59:53,255 calibrate.py _nudge_pos():1806 [1] 478: 0.130 -0.0000335 -0.0000356 2520 8.40 -0.592 -0.785 2008-05-19T23:46:18.049889792 INFO 2025-06-26 13:59:53,851 calibrate.py _nudge_pos():1806 [1] 537: 0.130 -0.0001289 0.0005078 9850 32.83 -0.582 2.866 2008-05-20T00:20:06.050962176 INFO 2025-06-26 13:59:54,343 calibrate.py _nudge_pos():1806 [1] 585: 0.130 0.0000355 -0.0000654 2074 6.91 0.762 -1.752 2008-05-20T00:27:48.049313024 INFO 2025-06-26 13:59:55,115 calibrate.py _nudge_pos():1806 [1] 661: 0.130 0.0000408 -0.0002224 9735 32.45 0.187 -1.270 2008-05-20T01:01:30.050796544 INFO 2025-06-26 13:59:55,758 calibrate.py _nudge_pos():1806 [1] 724: 0.150 0.0024583 0.0027691 12620 42.06 8.669 12.199 2008-05-20T01:44:36.043643904 INFO 2025-06-26 13:59:56,299 calibrate.py _nudge_pos():1806 [1] 777: 0.140 0.0002293 -0.0004409 11140 37.13 0.916 -2.200 2008-05-20T02:22:36.047452928 INFO 2025-06-26 13:59:56,961 calibrate.py _nudge_pos():1806 [1] 842: 0.140 -0.0000072 -0.0000146 2410 8.03 -0.133 -0.336 2008-05-20T02:31:42.050049024 INFO 2025-06-26 13:59:57,460 calibrate.py _nudge_pos():1806 [1] 890: 0.160 -0.0001255 0.0002467 9840 32.80 -0.567 1.394 2008-05-20T03:05:18.041944320 INFO 2025-06-26 13:59:58,080 calibrate.py _nudge_pos():1806 [1] 948: 0.150 0.0000339 -0.0000161 2115 7.05 0.714 -0.423 2008-05-20T03:13:18.049061632 INFO 2025-06-26 13:59:58,668 calibrate.py _nudge_pos():1806 [1] 1004: 0.150 0.0001634 -0.0002390 10075 33.58 0.721 -1.319 2008-05-20T03:47:48.047256832 INFO 2025-06-26 13:59:59,373 calibrate.py _nudge_pos():1806 [1] 1070: 0.150 0.0000190 -0.0000822 2735 9.11 0.310 -1.671 2008-05-20T03:58:00.045332224 INFO 2025-06-26 14:00:00,126 calibrate.py _nudge_pos():1806 [1] 1142: 0.150 0.0000390 -0.0000062 15 0.05 124.002 -24.539 2008-05-20T03:59:14.050262528 INFO 2025-06-26 14:00:00,159 calibrate.py _nudge_pos():1806 [1] 1145: 0.150 -0.0002132 0.0003136 9880 32.93 -0.960 1.765 2008-05-20T04:32:12.044760832 INFO 2025-06-26 14:00:00,805 calibrate.py _nudge_pos():1806 [1] 1205: 0.160 0.0000192 -0.0000324 2555 8.51 0.334 -0.705 2008-05-20T04:41:42.045712896 INFO 2025-06-26 14:00:01,443 calibrate.py _nudge_pos():1806 [1] 1264: 0.160 -0.0000355 -0.0000645 15 0.05 -112.827 -256.129 2008-05-20T04:42:43.041534464 INFO 2025-06-26 14:00:01,466 calibrate.py _nudge_pos():1806 [1] 1266: 0.170 0.0001280 -0.0001395 9860 32.86 0.577 -0.787 2008-05-20T05:15:36.046374400 INFO 2025-06-26 14:00:02,168 calibrate.py _nudge_pos():1806 [1] 1328: 0.170 0.0024060 0.0027959 12955 43.18 8.265 11.998 2008-05-20T05:59:48.044699904 INFO 2025-06-26 14:00:02,999 calibrate.py _nudge_pos():1806 [1] 1396: 0.160 0.0003020 -0.0003398 10975 36.58 1.225 -1.721 2008-05-20T06:37:30.049742080 INFO 2025-06-26 14:00:03,771 calibrate.py _nudge_pos():1806 [1] 1461: 0.160 -0.0000292 -0.0000139 2260 7.53 -0.574 -0.341 2008-05-20T06:46:06.044393984 INFO 2025-06-26 14:00:04,462 calibrate.py _nudge_pos():1806 [1] 1522: 0.170 -0.0003206 0.0001303 11010 36.70 -1.296 0.658 2008-05-20T07:23:48.049435904 INFO 2025-06-26 14:00:05,299 calibrate.py _nudge_pos():1806 [1] 1594: 0.170 0.0000305 0.0000125 2165 7.21 0.628 0.321 2008-05-20T07:32:12.044910080 INFO 2025-06-26 14:00:06,059 calibrate.py _nudge_pos():1806 [1] 1657: 0.170 0.0002136 -0.0002203 10370 34.56 0.917 -1.181 2008-05-20T08:07:48.048583680 INFO 2025-06-26 14:00:06,731 calibrate.py _nudge_pos():1806 [1] 1717: 0.170 0.0000044 -0.0000258 2465 8.21 0.080 -0.582 2008-05-20T08:17:00.050768896 INFO 2025-06-26 14:00:07,618 calibrate.py _nudge_pos():1806 [1] 1795: 0.170 -0.0002773 0.0005619 10925 36.41 -1.129 2.859 2008-05-20T08:54:42.045811712 INFO 2025-06-26 14:00:08,318 calibrate.py _nudge_pos():1806 [1] 1857: 0.170 0.0000237 -0.0000023 2035 6.78 0.518 -0.063 2008-05-20T09:02:30.043751424 INFO 2025-06-26 14:00:09,051 calibrate.py _nudge_pos():1806 [1] 1918: 0.170 0.0000130 -0.0000093 20 0.06 30.439 -27.091 2008-05-20T09:03:34.049367040 INFO 2025-06-26 14:00:09,104 calibrate.py _nudge_pos():1806 [1] 1922: 0.170 0.0001167 -0.0002126 9985 33.28 0.520 -1.184 2008-05-20T09:36:54.042358016 INFO 2025-06-26 14:00:09,961 calibrate.py _nudge_pos():1806 [1] 1994: 0.170 0.0022954 0.0027187 13805 46.01 7.399 10.949 2008-05-20T10:24:06.048352256 INFO 2025-06-26 14:00:10,636 calibrate.py _nudge_pos():1806 [1] 2048: 0.170 0.0002846 -0.0003836 10625 35.41 1.192 -2.007 2008-05-20T11:00:24.049148928 INFO 2025-06-26 14:00:11,405 calibrate.py _nudge_pos():1806 [1] 2113: 0.170 -0.0000235 0.0000179 2470 8.23 -0.424 0.404 2008-05-20T11:09:42.050923264 INFO 2025-06-26 14:00:12,146 calibrate.py _nudge_pos():1806 [1] 2177: 0.190 -0.0002768 0.0002556 9725 32.41 -1.266 1.461 2008-05-20T11:43:10.043366400 INFO 2025-06-26 14:00:12,937 calibrate.py _nudge_pos():1806 [1] 2246: 0.190 0.0000661 -0.0000297 1980 6.60 1.485 -0.834 2008-05-20T11:50:54.041580288 INFO 2025-06-26 14:00:12,985 calibrate.py _nudge_pos():1806 [1] 2250: 0.180 0.0000108 -0.0000064 75 0.25 6.477 -4.772 2008-05-20T11:51:12.050346496 INFO 2025-06-26 14:00:13,663 calibrate.py _nudge_pos():1806 [1] 2309: 0.180 0.0001933 -0.0002049 9970 33.23 0.863 -1.143 2008-05-20T12:25:24.049775104 INFO 2025-06-26 14:00:14,326 calibrate.py _nudge_pos():1806 [1] 2366: 0.190 -0.0000181 0.0000046 2420 8.06 -0.333 0.105 2008-05-20T12:34:24.042782976 INFO 2025-06-26 14:00:14,956 calibrate.py _nudge_pos():1806 [1] 2421: 0.190 -0.0003045 0.0003872 9840 32.80 -1.377 2.188 2008-05-20T13:08:06.044266496 INFO 2025-06-26 14:00:15,676 calibrate.py _nudge_pos():1806 [1] 2480: 0.190 0.0000316 -0.0000055 1690 5.63 0.832 -0.180 2008-05-20T13:14:42.047138304 INFO 2025-06-26 14:00:16,513 calibrate.py _nudge_pos():1806 [1] 2551: 0.190 0.0001688 -0.0002846 9820 32.73 0.765 -1.611 2008-05-20T13:48:36.047799808 INFO 2025-06-26 14:00:17,280 calibrate.py _nudge_pos():1806 [1] 2618: 0.180 0.0025833 0.0029305 13350 44.50 8.611 12.203 2008-05-20T14:34:12.050370816 INFO 2025-06-26 14:00:18,026 calibrate.py _nudge_pos():1806 [1] 2683: 0.190 0.0002463 -0.0004641 12130 40.43 0.904 -2.127 2008-05-20T15:15:42.049794048 INFO 2025-06-26 14:00:18,719 calibrate.py _nudge_pos():1806 [1] 2744: 0.190 0.0000283 -0.0000104 2430 8.10 0.519 -0.239 2008-05-20T15:24:48.042391040 INFO 2025-06-26 14:00:19,456 calibrate.py _nudge_pos():1806 [1] 2808: 0.200 -0.0000086 0.0005871 9165 30.55 -0.042 3.562 2008-05-20T15:56:24.042506240 INFO 2025-06-26 14:00:20,130 calibrate.py _nudge_pos():1806 [1] 2866: 0.190 0.0000577 -0.0000349 1635 5.45 1.571 -1.188 2008-05-20T16:02:48.046200064 INFO 2025-06-26 14:00:20,803 calibrate.py _nudge_pos():1806 [1] 2924: 0.200 0.0001060 -0.0001353 5865 19.55 0.804 -1.282 2008-05-20T16:23:18.041939456 INFO 2025-06-26 14:00:20,828 calibrate.py _nudge_pos():1806 [1] 2926: 0.190 -0.0000033 -0.0000063 84 0.28 -1.786 -4.209 2008-05-20T16:23:36.050705920 INFO 2025-06-26 14:00:21,459 calibrate.py _nudge_pos():1806 [1] 2979: 0.190 0.0001769 -0.0000637 5830 19.43 1.350 -0.607 2008-05-20T16:43:54.047267328 INFO 2025-06-26 14:00:22,300 calibrate.py _nudge_pos():1806 [1] 3043: 0.200 0.0000575 -0.0000940 2594 8.64 0.986 -2.015 2008-05-20T16:53:36.047397632 INFO 2025-06-26 14:00:22,917 calibrate.py _nudge_pos():1806 [1] 3096: 0.200 -0.0000442 0.0006308 9219 30.73 -0.213 3.804 2008-05-20T17:25:12.047512832 INFO 2025-06-26 14:00:23,614 calibrate.py _nudge_pos():1806 [1] 3156: 0.200 0.0000575 0.0000164 2074 6.91 1.234 0.441 2008-05-20T17:33:06.045041920 INFO 2025-06-26 14:00:24,240 calibrate.py _nudge_pos():1806 [1] 3210: 0.200 0.0001935 -0.0002254 10835 36.11 0.795 -1.157 2008-05-20T18:10:06.042961408 INFO 2025-06-26 14:00:24,978 calibrate.py _nudge_pos():1806 [1] 3274: 0.200 0.0000274 -0.0000039 404 1.34 3.024 -0.537 2008-05-20T18:12:30.043096832 INFO 2025-06-26 14:00:25,002 calibrate.py _nudge_pos():1806 [1] 3276: 0.200 0.0000351 -0.0000030 84 0.28 18.803 -1.991 2008-05-20T18:12:48.041863680 INFO 2025-06-26 14:00:25,912 calibrate.py _nudge_pos():1862 [1] 3326: - - - 3 0.01 - - INFO 2025-06-26 14:00:25,912 calibrate.py _nudge_pos():1868 [1] Points in final series = 374468 WARNING 2025-06-26 14:00:26,493 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:01:06,906 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:01:28,963 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 44 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:01:31,218 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 44 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:01:31,223 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.140.00/ctd1.nc INFO 2025-06-26 14:01:31,224 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:01:31,225 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 14:01:31,225 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:01:48,053 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:01:50,335 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:01:50,340 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.140.00/ctd2.nc INFO 2025-06-26 14:01:50,341 calibrate.py _range_qc_combined_nc():898 [1] Setting 167 ctd2_salinity values to NaN INFO 2025-06-26 14:01:50,342 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 14:01:50,342 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:01:53,198 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:01:56,775 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069 3070 3071 3072 3073 3074 3075 3076 3077 3078 3079 3080 3081 3082 3083 3084 3085 3086 3087 3088 3089 13920 33720 33721 33722 50100 56340 69660 69661 81180 194220 204480 258660 597060 617880 617881 617882 761460 762120 872820 873060 873720 875700 920280 989220 1098720 1216260 1216680 1326120 1326540 1327680 1330800 1406520 1406521 1440000 1440001 1440002 1551660 2007780 2363400 2459880 2585100 2688000 2688001 2799300 2913960 3402960 3402961 3454800 3482460 3877980 3877981 4135740 4135741 4354440 4354441 4354442] INFO 2025-06-26 14:01:57,464 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -8 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:01:57,472 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 14:01:57,482 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.140.00 INFO 2025-06-26 14:01:57,543 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_cal.nc INFO 2025-06-26 14:02:21,147 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, 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 14:02:21,153 process.py align():251 [1] Alignment steps for 2008.140.00 INFO 2025-06-26 14:02:21,199 align.py process_cal():139 [1] Processing dorado_2008.140.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.140.00 INFO 2025-06-26 14:02:21,296 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:02:21,306 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:02:21,570 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:02:21,588 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:02:21,819 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:02:21,836 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:02:21,982 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:02:21,982 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:02:22,087 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:02:22,103 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:02:22,328 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:22,340 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:22,547 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:22,557 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:22,758 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:22,769 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:22,968 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:22,979 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:23,185 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:23,196 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:23,403 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:23,414 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:23,614 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:23,626 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:23,825 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:23,836 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:24,037 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:24,049 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:24,248 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:24,261 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:24,460 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:24,472 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:24,669 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:24,680 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:24,879 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:24,889 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:25,090 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:25,102 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:25,302 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:25,313 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:25,511 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:25,523 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:25,724 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:25,735 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:25,936 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:25,951 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:26,152 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:26,164 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:26,364 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:02:26,374 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:02:26,613 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 14:02:26,763 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 14:02:26,915 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 14:02:27,074 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:02:27,230 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = nan INFO 2025-06-26 14:02:27,357 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = nan INFO 2025-06-26 14:02:27,483 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = nan INFO 2025-06-26 14:02:27,609 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = nan INFO 2025-06-26 14:02:27,737 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = nan INFO 2025-06-26 14:02:27,866 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 14:02:27,914 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_align.nc INFO 2025-06-26 14:02:28,083 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, 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 14:02:28,086 process.py resample():273 [1] Resampling steps for 2008.140.00 INFO 2025-06-26 14:02:28,086 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:02:28,123 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_align.nc mission netCDF file INFO 2025-06-26 14:02:28,133 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_align.nc mission netCDF file INFO 2025-06-26 14:02:28,135 resample.py get_mission_start_end():1145 [1] navigation: 2008-05-19T21:24:49.091423232 to 2008-05-20T18:14:07.846396672 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 14:02:28,138 resample.py get_mission_start_end():1145 [1] hs2 : 2008-05-19T21:24:23.513175552 to 2008-05-20T18:14:07.756402944 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 14:02:28,141 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-05-19T21:25:07.740145664 to 2008-05-20T18:14:07.876394752 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:02:28,144 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-05-19T21:24:43.371814912 to 2008-05-20T18:14:07.876394752 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:02:28,146 resample.py get_mission_start_end():1145 [1] isus : 2008-05-19T21:25:16.949514752 to 2008-05-20T18:14:07.836397312 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 14:02:28,147 resample.py get_mission_start_end():1145 [1] biolume : 2008-05-19T21:24:15.983657216 to 2008-05-20T18:14:06.886428416 (0 days 00:00:00.989966336 before mission_end) INFO 2025-06-26 14:02:28,149 resample.py get_mission_start_end():1145 [1] lopc : 2008-05-19T21:25:01.073171456 to 2008-05-19T21:25:01.073171456 (0 days 20:49:06.803223296 before mission_end) WARNING 2025-06-26 14:02:28,150 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 20:49:06.803223296 INFO 2025-06-26 14:02:28,151 resample.py get_mission_start_end():1145 [1] tailcone : 2008-05-19T21:24:20.713367296 to 2008-05-20T18:14:07.706406400 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 14:02:28,152 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_align.nc mission netCDF file INFO 2025-06-26 14:02:28,152 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:28,918 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,040 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,159 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,278 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,379 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,481 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,581 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,681 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,773 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,864 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:29,955 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,048 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,139 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,231 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,323 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,414 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,510 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,611 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,715 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,813 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:30,914 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,012 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,050 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,082 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,113 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,149 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,165 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,165 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 20:49:06.803223296 of NaNs to the end of mission INFO 2025-06-26 14:02:31,178 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,178 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 20:49:06.803223296 of NaNs to the end of mission INFO 2025-06-26 14:02:31,190 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,190 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 20:49:06.803223296 of NaNs to the end of mission INFO 2025-06-26 14:02:31,201 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,201 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 20:49:06.803223296 of NaNs to the end of mission INFO 2025-06-26 14:02:31,212 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,212 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 20:49:06.803223296 of NaNs to the end of mission INFO 2025-06-26 14:02:31,244 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:02:31,776 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_1S.nc INFO 2025-06-26 14:02:36,002 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 14:02:47,566 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.140.00/dorado_2008.140.00_1S_Gulper.txt INFO 2025-06-26 14:02:47,566 process.py archive():337 [1] Archiving steps for 2008.140.00 INFO 2025-06-26 14:02:47,566 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00, BASE_PATH = /data/auv_data INFO 2025-06-26 14:02:47,568 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 14:02:47,569 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.140.00_1S.nc INFO 2025-06-26 14:02:47,628 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:02:47,629 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.140.00_cal.nc INFO 2025-06-26 14:02:47,897 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:02:47,899 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.140.00_align.nc INFO 2025-06-26 14:02:48,146 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:02:48,219 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,294 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,300 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,352 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,564 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,575 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,664 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,680 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,882 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,888 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008140/2008.140.00 done. INFO 2025-06-26 14:02:48,889 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:02:48,890 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.140.00_1S_Gulper.txt INFO 2025-06-26 14:02:48,895 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.140.00/dorado_2008.140.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 14:02:48,895 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.140.00/dorado_2008.140.00_processing.log /Volumes/AUVCTD/surveys/2008/netcdf