INFO 2025-06-26 14:24:01,736 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 14:24:01,736 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - North bay shelf survey - ctdToUse = ctd2 INFO 2025-06-26 14:24:01,737 process.py process_mission():449 [1] Processing AUVCTD mission 2008.295.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:24:01,737 process.py download_process():165 [1] Download and processing steps for 2008.295.01 INFO 2025-06-26 14:24:01,737 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008295/2008.295.01 INFO 2025-06-26 14:24:01,737 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008295/2008.295.01 to /data/auv_data/dorado/missionlogs/2008.295.01 INFO 2025-06-26 14:24:08,529 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.295.01 INFO 2025-06-26 14:24:08,529 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/ctdDriver.log (21802308 bytes) INFO 2025-06-26 14:24:10,346 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/ctdDriver2.log (21802213 bytes) INFO 2025-06-26 14:24:12,213 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/gps.log (209156 bytes) INFO 2025-06-26 14:24:12,246 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/hydroscatlog.log (20806738 bytes) INFO 2025-06-26 14:24:14,520 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.295.01/hydroscatlog.log: [11918] INFO 2025-06-26 14:24:14,641 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/navigation.log (73070210 bytes) INFO 2025-06-26 14:24:20,810 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/isuslog.log (1439861 bytes) INFO 2025-06-26 14:24:20,963 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/parosci.log (25378646 bytes) INFO 2025-06-26 14:24:23,116 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/tailCone.log (3007387 bytes) INFO 2025-06-26 14:24:23,487 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/biolume.log (16858700 bytes) INFO 2025-06-26 14:24:25,114 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:24:26,007 logs2netcdfs.py download_process_logs():807 [1] Time to process: 17.48 seconds INFO 2025-06-26 14:24:26,008 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2008.295.01/lopc.bin (35603997 bytes) INFO 2025-06-26 14:24:26,008 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:24:26 2025 INFO 2025-06-26 14:24:26,008 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.295.01/parosci.nc INFO 2025-06-26 14:24:26,008 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:24:26,008 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.295.01/parosci.nc INFO 2025-06-26 14:24:26,012 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1224626417.3, sensor_off_time = 1224688379.5 INFO 2025-06-26 14:24:26,012 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 61962 seconds. Expecting to read 123924 L frames from the lopc.bin file. INFO 2025-06-26 14:24:26,012 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 123924 records from the lopc.bin file. INFO 2025-06-26 14:24:26,764 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2008-10-21 22:00:17 Z and endTime = 2008-10-22 15:12:59 Z with 123924 records expected to be read from lopc.bin INFO 2025-06-26 14:24:26,764 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2008.295.01/lopc.bin INFO 2025-06-26 14:24:26,765 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2008.295.01/lopc.nc INFO 2025-06-26 14:24:26,765 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2008.295.01/lopc.nc INFO 2025-06-26 14:24:26,766 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2008.295.01 INFO 2025-06-26 14:24:26,766 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 14:24:26,798 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x84 in position 0: invalid start byte INFO 2025-06-26 14:24:26,799 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 14:24:26,799 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.295.01/parosci.nc INFO 2025-06-26 14:24:26,799 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:24:26,799 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.295.01/parosci.nc INFO 2025-06-26 14:24:26,802 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1224626417.3, sensor_off_time = 1224688379.5 INFO 2025-06-26 14:24:26,802 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 61962 seconds. Expecting to read 123924 L frames from the lopc.bin file. INFO 2025-06-26 14:24:26,802 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 123924 records from the lopc.bin file. INFO 2025-06-26 14:24:26,803 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 9893 and len(sampleCountList) = 24 INFO 2025-06-26 14:24:26,803 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 14:24:26,803 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [9893 9894 9895 9896 9897 9898 9899 9907 9908 9909 9910 9911 9921 9922 9923 9924 9925 9926 9927 9928 9937 9938 9939 9940] INFO 2025-06-26 14:24:26,803 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 14:24:26,803 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 14:24:26,804 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 1 1 1 1 8 1 1 1 1 10 1 1 1 1 1 1 1 9 1 1 1] INFO 2025-06-26 14:24:26,804 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 14:24:26,804 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [9893 9894 9895 9896 9897 9898 9899 9907 9908 9909 9910 9911 9921 9922 9923 9924 9925 9926 9927 9928 9937 9938 9939 9940] INFO 2025-06-26 14:24:26,804 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [9893 9894 9895 9896 9897 9898 9899 9907 9908 9909 9910 9911 9921 9922 9923 9924 9925 9926 9927 9928 9937 9938 9939 9940] with len(correctedSampleCountList) = 24 INFO 2025-06-26 14:24:26,805 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 9893 from all values of correctedSampleCountList INFO 2025-06-26 14:24:26,805 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 14:24:26,805 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [ 0. 0.5 1. 1.5 2. 2.5 3. 7. 7.5 8. 8.5 9. 14. 14.5 15. 15.5 16. 16.5 17. 17.5 22. 22.5 23. 23.5] INFO 2025-06-26 14:24:26,805 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.22462642e+09 1.22462642e+09 1.22462642e+09 1.22462642e+09 1.22462642e+09 1.22462642e+09 1.22462642e+09 1.22462642e+09 1.22462642e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462643e+09 1.22462644e+09 1.22462644e+09 1.22462644e+09 1.22462644e+09] INFO 2025-06-26 14:24:26,806 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1224626417.3 1224626417.8, ..., timestampArray[-2:] = 1224626440.3 1224626440.8] INFO 2025-06-26 14:24:26,806 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1224626417.284815), np.float64(1224626417.784815)], ..., timestampList[-2:] = [np.float64(1224626440.284815), np.float64(1224626440.784815)]] INFO 2025-06-26 14:24:26,806 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 24) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:24:26,806 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20], ... lFrameCountWrittenList[-2:] = [20] INFO 2025-06-26 14:24:26,806 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 1 INFO 2025-06-26 14:24:26,806 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 24 INFO 2025-06-26 14:24:26,806 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1224626417.284815), np.float64(1224626417.784815)], ..., timestampList[-2:] = [np.float64(1224626440.284815), np.float64(1224626440.784815)]] INFO 2025-06-26 14:24:26,807 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 24) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:24:26,807 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19)] ... [np.int32(19)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 14:24:26,807 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 1 INFO 2025-06-26 14:24:26,807 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 14:24:26,807 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 14:24:26,808 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 1 INFO 2025-06-26 14:24:26,808 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1224626434.784815)], ..., tsList[-2:] = [np.float64(1224626434.784815)] INFO 2025-06-26 14:24:26,809 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2008-10-21 22:00:34 Z INFO 2025-06-26 14:24:26,809 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2008-10-21 22:00:34 Z INFO 2025-06-26 14:24:26,809 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 24 INFO 2025-06-26 14:24:26,809 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 14:24:26,809 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:24:26,809 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:24:26,813 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2008.295.01/lopc.nc INFO 2025-06-26 14:24:26,813 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 14:24:26 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 14:24:26,815 process.py calibrate():227 [1] Calibration steps for 2008.295.01 INFO 2025-06-26 14:24:27,390 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 14:24:27,392 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:24:28,417 calibrate.py _nudge_pos():1806 [1] 124: 0.200 -0.0003348 0.0003929 773 2.58 -19.278 28.254 2008-10-21T22:04:54.115851008 INFO 2025-06-26 14:24:29,069 calibrate.py _nudge_pos():1806 [1] 189: 0.010 -0.0011232 0.0008940 9487 31.63 -5.267 5.238 2008-10-21T22:37:36.321430528 INFO 2025-06-26 14:24:29,139 calibrate.py _nudge_pos():1806 [1] 196: 0.010 0.0000031 -0.0000074 70 0.23 1.975 -5.946 2008-10-21T22:37:56.320060416 INFO 2025-06-26 14:24:29,808 calibrate.py _nudge_pos():1806 [1] 262: 0.010 -0.0001457 0.0002165 9714 32.38 -0.668 1.239 2008-10-21T23:11:24.322502912 INFO 2025-06-26 14:24:30,533 calibrate.py _nudge_pos():1806 [1] 334: 0.020 0.0000476 0.0000574 5044 16.81 0.420 0.632 2008-10-21T23:29:24.318518272 INFO 2025-06-26 14:24:31,170 calibrate.py _nudge_pos():1806 [1] 393: 0.020 0.0000273 -0.0000899 4089 13.63 0.298 -1.222 2008-10-21T23:44:00.318508032 INFO 2025-06-26 14:24:31,850 calibrate.py _nudge_pos():1806 [1] 461: 0.030 -0.0000207 0.0000028 2365 7.88 -0.389 0.065 2008-10-21T23:53:00.321515264 INFO 2025-06-26 14:24:32,465 calibrate.py _nudge_pos():1806 [1] 523: 0.030 0.0000245 0.0001988 4194 13.98 0.260 2.635 2008-10-22T00:08:00.319861248 INFO 2025-06-26 14:24:33,169 calibrate.py _nudge_pos():1806 [1] 593: 0.030 0.0000304 -0.0000502 2205 7.35 0.614 -1.265 2008-10-22T00:16:30.314924288 INFO 2025-06-26 14:24:33,265 calibrate.py _nudge_pos():1806 [1] 602: 0.030 0.0000571 0.0000663 40 0.13 65.167 94.442 2008-10-22T00:16:46.313828352 INFO 2025-06-26 14:24:33,667 calibrate.py _nudge_pos():1806 [1] 642: 0.030 0.0000262 -0.0000121 4734 15.78 0.246 -0.142 2008-10-22T00:33:12.316282368 INFO 2025-06-26 14:24:34,319 calibrate.py _nudge_pos():1806 [1] 708: 0.040 0.0001958 0.0000118 9754 32.51 0.893 0.067 2008-10-22T01:06:48.318176768 INFO 2025-06-26 14:24:34,791 calibrate.py _nudge_pos():1806 [1] 755: 0.040 0.0000010 0.0000016 20 0.06 2.351 4.757 2008-10-22T01:07:38.314751744 INFO 2025-06-26 14:24:35,057 calibrate.py _nudge_pos():1806 [1] 781: 0.050 0.0002169 -0.0000010 9734 32.45 0.991 -0.006 2008-10-22T01:40:30.319660288 INFO 2025-06-26 14:24:35,432 calibrate.py _nudge_pos():1806 [1] 818: 0.060 0.0002719 0.0000382 9509 31.70 1.271 0.223 2008-10-22T02:12:48.316898304 INFO 2025-06-26 14:24:36,118 calibrate.py _nudge_pos():1806 [1] 886: 0.070 0.0002703 0.0000771 9444 31.48 1.272 0.454 2008-10-22T02:45:24.312903424 INFO 2025-06-26 14:24:36,839 calibrate.py _nudge_pos():1806 [1] 955: 0.070 0.0002148 -0.0000110 9199 30.66 1.038 -0.066 2008-10-22T03:17:12.322195712 INFO 2025-06-26 14:24:37,569 calibrate.py _nudge_pos():1806 [1] 1026: 0.070 -0.0000188 -0.0000297 700 2.33 -1.193 -2.363 2008-10-22T03:20:42.317810176 INFO 2025-06-26 14:24:38,095 calibrate.py _nudge_pos():1806 [1] 1076: 0.080 0.0000411 0.0003276 4554 15.18 0.401 3.999 2008-10-22T03:36:42.322045440 INFO 2025-06-26 14:24:38,622 calibrate.py _nudge_pos():1806 [1] 1127: 0.080 0.0013468 0.0000861 3020 10.06 19.824 1.586 2008-10-22T03:47:36.317243648 INFO 2025-06-26 14:24:39,169 calibrate.py _nudge_pos():1806 [1] 1180: 0.090 0.0000295 -0.0000229 4569 15.23 0.287 -0.279 2008-10-22T04:03:42.321067776 INFO 2025-06-26 14:24:39,716 calibrate.py _nudge_pos():1806 [1] 1233: 0.080 0.0011795 0.0000675 2860 9.53 18.333 1.313 2008-10-22T04:14:06.318320896 INFO 2025-06-26 14:24:39,727 calibrate.py _nudge_pos():1806 [1] 1234: 0.080 -0.0000016 0.0000036 15 0.05 -4.938 14.483 2008-10-22T04:14:09.318115584 INFO 2025-06-26 14:24:39,749 calibrate.py _nudge_pos():1806 [1] 1236: 0.080 -0.0000306 0.0000307 15 0.05 -97.281 122.006 2008-10-22T04:14:13.317841408 INFO 2025-06-26 14:24:40,261 calibrate.py _nudge_pos():1806 [1] 1285: 0.090 -0.0000875 0.0002857 4404 14.68 -0.883 3.606 2008-10-22T04:29:42.314200832 INFO 2025-06-26 14:24:40,295 calibrate.py _nudge_pos():1806 [1] 1288: 0.080 -0.0000013 -0.0000127 80 0.26 -0.713 -8.946 2008-10-22T04:30:00.312967680 INFO 2025-06-26 14:24:40,962 calibrate.py _nudge_pos():1806 [1] 1342: 0.090 0.0043916 0.0021091 11134 37.11 17.533 10.530 2008-10-22T05:08:00.316776960 INFO 2025-06-26 14:24:41,547 calibrate.py _nudge_pos():1806 [1] 1395: 0.100 0.0049197 0.0021027 11619 38.73 18.828 10.060 2008-10-22T05:47:36.314009856 INFO 2025-06-26 14:24:42,104 calibrate.py _nudge_pos():1806 [1] 1447: 0.110 0.0047453 0.0018559 10843 36.15 19.464 9.514 2008-10-22T06:24:36.321928960 INFO 2025-06-26 14:24:42,137 calibrate.py _nudge_pos():1806 [1] 1450: 0.110 -0.0000160 0.0000123 85 0.28 -8.483 8.141 2008-10-22T06:24:55.320627456 INFO 2025-06-26 14:24:42,660 calibrate.py _nudge_pos():1806 [1] 1500: 0.110 0.0047518 0.0018948 11059 36.86 19.118 9.524 2008-10-22T07:02:36.315738624 INFO 2025-06-26 14:24:43,189 calibrate.py _nudge_pos():1806 [1] 1550: 0.110 0.0013889 0.0003383 3175 10.58 19.471 5.926 2008-10-22T07:14:00.318881280 INFO 2025-06-26 14:24:43,711 calibrate.py _nudge_pos():1806 [1] 1600: 0.120 0.0000298 -0.0000254 5004 16.68 0.265 -0.283 2008-10-22T07:31:30.316951552 INFO 2025-06-26 14:24:44,286 calibrate.py _nudge_pos():1806 [1] 1655: 0.120 -0.0000195 0.0000139 2160 7.20 -0.401 0.358 2008-10-22T07:39:36.313658368 INFO 2025-06-26 14:24:44,810 calibrate.py _nudge_pos():1806 [1] 1705: 0.120 0.0000136 0.0002640 4555 15.18 0.133 3.223 2008-10-22T07:55:36.317893632 INFO 2025-06-26 14:24:45,397 calibrate.py _nudge_pos():1806 [1] 1761: 0.130 0.0000188 0.0000132 2275 7.58 0.369 0.323 2008-10-22T08:04:06.312956672 INFO 2025-06-26 14:24:45,943 calibrate.py _nudge_pos():1806 [1] 1813: 0.120 0.0000671 0.0000107 4964 16.55 0.601 0.120 2008-10-22T08:21:30.321437184 INFO 2025-06-26 14:24:46,424 calibrate.py _nudge_pos():1806 [1] 1859: 0.130 0.0002093 0.0000642 9644 32.15 0.965 0.370 2008-10-22T08:54:24.316209408 INFO 2025-06-26 14:24:47,129 calibrate.py _nudge_pos():1806 [1] 1925: 0.130 0.0001846 0.0000755 9484 31.61 0.865 0.443 2008-10-22T09:27:06.321802496 INFO 2025-06-26 14:24:47,162 calibrate.py _nudge_pos():1806 [1] 1928: 0.140 -0.0000049 -0.0000280 140 0.46 -1.564 -11.180 2008-10-22T09:27:36.319747584 INFO 2025-06-26 14:24:47,669 calibrate.py _nudge_pos():1806 [1] 1976: 0.140 0.0002586 0.0000697 9364 31.21 1.228 0.414 2008-10-22T09:59:36.318218752 INFO 2025-06-26 14:24:48,312 calibrate.py _nudge_pos():1806 [1] 2036: 0.150 0.0002222 0.0001926 9334 31.11 1.058 1.147 2008-10-22T10:31:42.316279040 INFO 2025-06-26 14:24:49,031 calibrate.py _nudge_pos():1806 [1] 2098: 0.160 0.0003203 0.0000717 9444 31.48 1.507 0.422 2008-10-22T11:04:12.312695040 INFO 2025-06-26 14:24:49,791 calibrate.py _nudge_pos():1806 [1] 2169: 0.150 0.0000744 0.0000457 1240 4.13 2.668 2.049 2008-10-22T11:09:30.320910080 INFO 2025-06-26 14:24:50,364 calibrate.py _nudge_pos():1806 [1] 2220: 0.160 0.0000541 0.0004123 5239 17.46 0.459 4.375 2008-10-22T11:27:48.315692032 INFO 2025-06-26 14:24:50,920 calibrate.py _nudge_pos():1806 [1] 2272: 0.160 0.0014177 0.0000990 3105 10.35 20.296 1.774 2008-10-22T11:39:00.319656704 INFO 2025-06-26 14:24:51,517 calibrate.py _nudge_pos():1806 [1] 2328: 0.170 0.0001325 0.0000803 5094 16.98 1.156 0.876 2008-10-22T11:56:54.316082944 INFO 2025-06-26 14:24:52,104 calibrate.py _nudge_pos():1806 [1] 2382: 0.160 0.0009832 0.0001094 2315 7.71 18.881 2.628 2008-10-22T12:05:30.320733952 INFO 2025-06-26 14:24:52,679 calibrate.py _nudge_pos():1806 [1] 2436: 0.180 -0.0000226 0.0002454 3784 12.61 -0.266 3.605 2008-10-22T12:19:00.315245568 INFO 2025-06-26 14:24:52,744 calibrate.py _nudge_pos():1806 [1] 2442: 0.180 0.0000063 0.0000129 75 0.25 3.754 9.729 2008-10-22T12:19:20.313875712 INFO 2025-06-26 14:24:53,206 calibrate.py _nudge_pos():1806 [1] 2485: 0.180 0.0046021 0.0020636 10639 35.46 19.228 10.782 2008-10-22T12:55:30.315220480 INFO 2025-06-26 14:24:53,218 calibrate.py _nudge_pos():1806 [1] 2486: 0.180 0.0000308 0.0000338 185 0.61 7.445 10.209 2008-10-22T12:56:07.312686080 INFO 2025-06-26 14:24:53,813 calibrate.py _nudge_pos():1806 [1] 2542: 0.180 0.0048383 0.0020222 10908 36.36 19.721 10.305 2008-10-22T13:33:24.319440384 INFO 2025-06-26 14:24:54,398 calibrate.py _nudge_pos():1806 [1] 2596: 0.190 0.0049849 0.0019674 11044 36.81 20.076 9.903 2008-10-22T14:11:06.314483200 INFO 2025-06-26 14:24:55,011 calibrate.py _nudge_pos():1806 [1] 2653: 0.200 0.0048371 0.0019146 10758 35.86 20.003 9.892 2008-10-22T14:47:54.313224704 INFO 2025-06-26 14:24:55,731 calibrate.py _nudge_pos():1806 [1] 2720: 0.200 0.0001641 0.0000080 3269 10.89 2.235 0.137 2008-10-22T14:59:54.313901312 INFO 2025-06-26 14:24:56,288 calibrate.py _nudge_pos():1806 [1] 2772: 0.200 0.0006416 0.0006401 3044 10.14 9.382 11.694 2008-10-22T15:10:54.318688256 INFO 2025-06-26 14:24:56,310 calibrate.py _nudge_pos():1806 [1] 2774: 0.200 -0.0000656 -0.0000676 29 0.09 -104.331 -134.138 2008-10-22T15:11:01.318208512 INFO 2025-06-26 14:24:57,584 calibrate.py _nudge_pos():1862 [1] 2860: - - - 0 0.00 - - INFO 2025-06-26 14:24:57,584 calibrate.py _nudge_pos():1868 [1] Points in final series = 309352 WARNING 2025-06-26 14:24:57,997 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:25:30,770 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:25:33,062 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:25:34,917 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:25:34,921 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.295.01/ctd1.nc INFO 2025-06-26 14:25:34,923 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:25:34,923 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 14:25:34,923 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:25:37,171 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:25:39,047 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:25:39,051 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.295.01/ctd2.nc INFO 2025-06-26 14:25:39,053 calibrate.py _range_qc_combined_nc():898 [1] Setting 177 ctd2_salinity values to NaN INFO 2025-06-26 14:25:39,053 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 14:25:39,053 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:25:39,141 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:25:42,040 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 72 120 2220 6480 6481 6482 8340 8341 8342 9660 9661 10800 10801 10802 12960 12961 12962 16140 16141 16142 16143 16144 16145 16146 16147 17100 17101 17102 36960 36961 36962 36963 36964 36965 36966 46800 46801 46802 46803 46804 46805 46806 52380 56040 56041 56042 60480 60481 60482 60483 60484 60485 60486 78540 78541 78542 78543 78544 78545 78546 89760 97620 97621 97622 97623 125340 125341 125342 125343 125344 125345 128940 128941 128942 128943 128944 128945 131280 131281 131282 133620 133621 133622 133623 179520 179521 179522 179523 179524 179525 179526 190920 190921 190922 190923 190924 190925 190926 190927 190928 190929 190930 199440 199441 199442 199443 199444 199445 199446 199447 199448 199449 219180 245700 245701 245702 245703 245704 245705 245706 245707 245708 245709 245710 245711 285960 285961 285962 285963 285964 285965 285966 285967 312600 312601 312602 312603 312604 312605 312606 355020 355021 355022 355023 355024 355025 452400 452401 452402 452403 452404 452405 452406 452407 452408 452409 452410 477300 477301 477302 477303 534060 534061 534062 534063 534064 534065 534066 534067 534068 577980 678660 678661 678662 678663 678664 678665 678666 678667 678668 678669 678670 678671 738540 738900 738901 738902 740160 740161 740162 740163 740164 740165 740166 740167 740168 758940 758941 758942 1034640 1034641 1034642 1034643 1034644 1034645 1034646 1037280 1037281 1140180 1140181 1140182 1140183 1140184 1140185 1140186 1140187 1140188 1158900 1158901 1158902 1208640 1208641 1208642 1208643 1208644 1208645 1273380 1273381 1273382 1273383 1288920 1288921 1288922 1288923 1288924 1335660 1335661 1335662 1335663 1335664 1335665 1335666 1335667 1335668 1335669 1433460 1433461 1433462 1433463 1433464 1433465 1548180 1548181 1548182 1548183 1548184 1548185 1548186 1555560 1555561 1555562 1555563 1555564 1555565 1633980 1633981 1633982 1633983 1633984 1633985 1633986 1633987 1633988 1770720 1770721 1770722 1770723 1770724 1770725 1780560 1783020 1783021 1783022 1783023 1783024 1786200 1786201 1786202 1786203 1786204 1786205 1786206 1886880 1886881 1886882 1886883 1886884 2012640 2012641 2012642 2012643 2012644 2012645 2201580 2201581 2201582 2201583 2201584 2201585 2201586 2201587 2201588 2261640 2261641 2261642 2261643 2435940 2670060 2670061 2670062 2670063 2670064 2670065 2670066 2670067 2679840 2679841 2679842 2679843 2679844 2894880 2894881 2894882 2894883 2951040 2951041 2951042 2951043 2951044 2951045 2969220 2969221 2969222 2969223 2969224 2969225 2969226 2969227 2969228 2969229 3095100 3095101 3095102 3095103 3095104 3095105 3095106 3095107 3095108 3095109 3095110 3095111 3195780 3195781 3195782 3195783 3195784 3195785 3195786 3195787 3195788 3257580 3609180 3609181 3609182 3609183 3700440 3700441 3700442] INFO 2025-06-26 14:25:42,606 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:25:42,613 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 14:25:42,624 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.295.01 INFO 2025-06-26 14:25:42,675 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_cal.nc INFO 2025-06-26 14:25:42,858 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 14:25:42,865 process.py align():251 [1] Alignment steps for 2008.295.01 INFO 2025-06-26 14:25:42,905 align.py process_cal():139 [1] Processing dorado_2008.295.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.295.01 INFO 2025-06-26 14:25:42,986 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:25:42,994 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:25:43,185 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:25:43,195 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:25:43,383 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:25:43,396 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:25:43,520 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:25:43,520 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:25:43,594 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:25:43,604 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:25:43,792 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:43,802 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:43,962 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:43,971 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:44,136 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:44,145 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:44,307 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:44,317 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:44,481 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:44,490 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:44,652 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:44,661 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:44,823 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:44,832 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:44,992 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:45,002 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:45,167 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:45,176 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:45,338 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:45,349 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:45,512 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:45,522 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:45,684 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:45,693 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:45,856 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:45,865 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:46,028 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:46,037 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:46,203 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:46,213 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:46,375 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:46,384 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:46,552 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:46,561 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:46,725 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:46,736 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:46,900 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:46,909 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:47,073 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:25:47,082 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:25:47,281 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:25:47,404 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:25:47,529 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:25:47,656 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:25:47,785 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = nan INFO 2025-06-26 14:25:47,891 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = nan INFO 2025-06-26 14:25:47,996 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = nan INFO 2025-06-26 14:25:48,102 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = nan INFO 2025-06-26 14:25:48,206 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = nan INFO 2025-06-26 14:25:48,314 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 14:25:48,355 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_align.nc INFO 2025-06-26 14:25:48,497 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 14:25:48,500 process.py resample():273 [1] Resampling steps for 2008.295.01 INFO 2025-06-26 14:25:48,500 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:25:48,535 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_align.nc mission netCDF file INFO 2025-06-26 14:25:48,543 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_align.nc mission netCDF file INFO 2025-06-26 14:25:48,545 resample.py get_mission_start_end():1145 [1] navigation: 2008-10-21T22:00:49.902580480 to 2008-10-22T15:12:59.520111104 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:25:48,548 resample.py get_mission_start_end():1145 [1] hs2 : 2008-10-21T22:00:26.604176640 to 2008-10-22T15:12:59.440116736 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 14:25:48,550 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-10-21T22:00:44.472952576 to 2008-10-22T15:12:59.520111104 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:25:48,553 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-10-21T22:00:44.232968960 to 2008-10-22T15:12:59.450115840 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 14:25:48,555 resample.py get_mission_start_end():1145 [1] isus : 2008-10-21T22:01:32.639652864 to 2008-10-22T15:12:59.110139136 (0 days 00:00:00.409971968 before mission_end) INFO 2025-06-26 14:25:48,556 resample.py get_mission_start_end():1145 [1] biolume : 2008-10-21T22:00:16.434839040 to 2008-10-22T15:12:58.750129664 (0 days 00:00:00.769981440 before mission_end) INFO 2025-06-26 14:25:48,557 resample.py get_mission_start_end():1145 [1] lopc : 2008-10-21T22:00:34.784815104 to 2008-10-21T22:00:34.784815104 (0 days 17:12:24.735296 before mission_end) WARNING 2025-06-26 14:25:48,558 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 17:12:24.735296 INFO 2025-06-26 14:25:48,559 resample.py get_mission_start_end():1145 [1] tailcone : 2008-10-21T22:00:22.544454912 to 2008-10-22T15:12:59.520111104 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:25:48,560 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_align.nc mission netCDF file INFO 2025-06-26 14:25:48,560 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,205 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,307 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,407 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,506 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,592 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,676 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,760 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,843 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:49,922 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,001 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,082 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,161 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,239 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,317 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,395 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,474 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,556 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,641 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,729 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,811 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,893 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:50,974 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,007 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,033 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,058 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,089 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,103 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,104 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 17:12:24.735296 of NaNs to the end of mission INFO 2025-06-26 14:25:51,115 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,115 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 17:12:24.735296 of NaNs to the end of mission INFO 2025-06-26 14:25:51,125 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,125 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 17:12:24.735296 of NaNs to the end of mission INFO 2025-06-26 14:25:51,135 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,136 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 17:12:24.735296 of NaNs to the end of mission INFO 2025-06-26 14:25:51,146 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,146 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 17:12:24.735296 of NaNs to the end of mission INFO 2025-06-26 14:25:51,172 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:25:51,647 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_1S.nc INFO 2025-06-26 14:25:56,188 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 14:26:11,076 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.295.01/dorado_2008.295.01_1S_Gulper.txt INFO 2025-06-26 14:26:11,077 process.py archive():337 [1] Archiving steps for 2008.295.01 INFO 2025-06-26 14:26:11,077 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01, BASE_PATH = /data/auv_data INFO 2025-06-26 14:26:11,078 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 14:26:11,079 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.295.01_1S.nc INFO 2025-06-26 14:26:11,128 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:26:11,129 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.295.01_cal.nc INFO 2025-06-26 14:26:11,354 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:26:11,355 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.295.01_align.nc INFO 2025-06-26 14:26:11,542 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:26:11,606 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:11,663 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:11,669 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:11,724 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:11,911 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:11,920 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:11,991 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:12,006 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:12,168 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:12,173 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008295/2008.295.01 done. INFO 2025-06-26 14:26:12,174 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:26:12,175 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.295.01_1S_Gulper.txt INFO 2025-06-26 14:26:12,180 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.295.01/dorado_2008.295.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 14:26:12,180 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.295.01/dorado_2008.295.01_processing.log /Volumes/AUVCTD/surveys/2008/netcdf