INFO 2025-06-26 16:55:12,326 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 16:55:12,326 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Inner-bay survey thirteenth - Overnight mirroring waveglider N-S across Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 16:55:12,327 process.py process_mission():449 [1] Processing AUVCTD mission 2010.298.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 16:55:12,327 process.py download_process():165 [1] Download and processing steps for 2010.298.01 INFO 2025-06-26 16:55:12,327 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010298/2010.298.01 INFO 2025-06-26 16:55:12,327 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010298/2010.298.01 to /data/auv_data/dorado/missionlogs/2010.298.01 INFO 2025-06-26 16:55:18,862 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.298.01 INFO 2025-06-26 16:55:18,862 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/ctdDriver.log (22267115 bytes) INFO 2025-06-26 16:55:20,414 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.298.01/ctdDriver.log: [ 56 481 566 701 729 967 987 1071 1106 1137 1496 1509 1580 1697 1726 2049 2210 2310 2455 2632 2656 4036 4358 4377 4852 6042 6574 8502 10815 11136 11930 12868 13627 14680 16721 16783 20189 22806 23141 23897 24290 26343 27018 29597 29861 30864 34301 37145 37731 40414 40591 42030 42031 43296 45985 46150 56621 56732 59578 61139 64511 66043 66861 70166 80021 90307 91406 95754 97494 103364 104607 115066 115977 117167 122148 122149 122588 123411 130067 130601 132153 133065 137115 137319 140195 147062 154297 154410 161401 161523 168639 170901 173129 174393 175068 178204 182567 183123 184168 184341 190885 191053 193751 197100 197565 200353 204213 204483 204551 211293 211328 212482 217917] INFO 2025-06-26 16:55:20,479 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/ctdDriver2.log (22266335 bytes) INFO 2025-06-26 16:55:22,006 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.298.01/ctdDriver2.log: [ 40 347 465 551 672 686 713 970 1054 1089 1090 1481 1494 1681 1710 2032 2034 2195 2295 2638 3238 4017 4357 4832 6021 6553 7781 7965 8480 11115 13607 14660 15457 16703 20171 22790 23881 24275 26327 29844 30847 34284 38967 40398 40576 42014 43280 45970 48888 54446 56608 63437 64501 66034 80015 88838 90305 90454 91403 97491 100706 103363 104605 117163 122144 122479 123409 130065 130599 133064 140773 141815 145153 147059 154294 154407 157434 157465 161397 161519 166996 168635 173124 178195 181029 182556 183112 184328 188836 191043 197089 197555 204204 204475 204543 211191 211285 211321 217908 224625] INFO 2025-06-26 16:55:22,081 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/gps.log (434948 bytes) INFO 2025-06-26 16:55:22,134 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/hydroscatlog.log (19492810 bytes) INFO 2025-06-26 16:55:24,090 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.298.01/hydroscatlog.log: [ 2 63 75 129 132 270 343 353 376 439 581 596 681 768 782 1048 1069 1110 1189 1449 1598 1666 1783 1813 2136 2148 2342 2401 2581 2722 2747 2983 3178 3512 3742 3818 4983 5402 5721 6669 7383 9701 10128 11236 11237 11300 11384 11851 12034 12974 14544 15242 16891 17775 18050 20294 21453 21782 23248 24004 24068 24398 26450 27125 30614 30770 31996 34406 34746 37253 37716 37782 37841 40524 41193 41194 43380 43406 47237 49016 49263 50126 54570 54920 56504 56734 56846 57150 57891 58213 63562 66159 66160 70281 76266 79742 80133 80486 81584 83380 83709 85156 87828 90420 90492 91125 91519 95866 97558 100184 100822 104723 104968 111046 111836 115179 116091 118947 121447 122596 122597 122702 123526 126066 126518 130183 133614 140293 141057 141723 147060 147176 152679 153479 155363 157549 161636 162688 166024 166164 173719 174501 177729 181146 181147 182672 183228 183584 184273 184446 188952 189296 190990 196503 196504 197205 197812 204588 204656 205170 208337 208338 210796 211396 211397 212588 218549 218582 220171 224734 224998 225663 227666 228353 231449 231504] INFO 2025-06-26 16:55:24,151 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/navigation.log (68332746 bytes) INFO 2025-06-26 16:55:29,080 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/isuslog.log (1440981 bytes) INFO 2025-06-26 16:55:29,220 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/parosci.log (25430342 bytes) INFO 2025-06-26 16:55:31,369 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/tailCone.log (13895275 bytes) INFO 2025-06-26 16:55:33,072 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/biolume.log (16215118 bytes) INFO 2025-06-26 16:55:34,675 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 16:55:35,475 logs2netcdfs.py download_process_logs():807 [1] Time to process: 16.61 seconds INFO 2025-06-26 16:55:35,475 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.298.01/lopc.bin (81341000 bytes) INFO 2025-06-26 16:55:35,475 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 16:55:35 2025 INFO 2025-06-26 16:55:35,475 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.298.01/parosci.nc INFO 2025-06-26 16:55:35,475 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:55:35,475 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.298.01/parosci.nc INFO 2025-06-26 16:55:35,479 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1288040885.2, sensor_off_time = 1288098936.3 INFO 2025-06-26 16:55:35,479 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 58051 seconds. Expecting to read 116102 L frames from the lopc.bin file. INFO 2025-06-26 16:55:35,479 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 116102 records from the lopc.bin file. INFO 2025-06-26 16:55:36,168 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-10-25 21:08:05 Z and endTime = 2010-10-26 13:15:36 Z with 116102 records expected to be read from lopc.bin INFO 2025-06-26 16:55:36,168 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.298.01/lopc.bin INFO 2025-06-26 16:55:36,168 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.298.01/lopc.nc INFO 2025-06-26 16:55:36,169 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.298.01/lopc.nc INFO 2025-06-26 16:55:36,169 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.298.01 INFO 2025-06-26 16:55:36,169 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 16:55:36,172 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A067598 WARNING 2025-06-26 16:55:36,172 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 16:55:36,223 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 16:55:36,223 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 16:55:36,223 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 16:55:43,042 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x85 in position 0: invalid start byte INFO 2025-06-26 16:55:43,042 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 16:55:43,043 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.298.01/parosci.nc INFO 2025-06-26 16:55:43,043 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:55:43,043 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.298.01/parosci.nc INFO 2025-06-26 16:55:43,046 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1288040885.2, sensor_off_time = 1288098936.3 INFO 2025-06-26 16:55:43,046 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 58051 seconds. Expecting to read 116102 L frames from the lopc.bin file. INFO 2025-06-26 16:55:43,046 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 116102 records from the lopc.bin file. INFO 2025-06-26 16:55:43,046 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 48519 and len(sampleCountList) = 8818 INFO 2025-06-26 16:55:43,047 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 16:55:43,047 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [48519 48520 48521 ... 57993 57994 57995] INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [4] INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 49180 at index = 4 INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [48519 48520 48521 ... 57993 57994 57995] INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [48519 48520 48521 ... 57993 57994 57995] with len(correctedSampleCountList) = 8818 INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 48519 from all values of correctedSampleCountList INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 16:55:43,048 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.0000e+00 5.0000e-01 1.0000e+00 ... 4.7370e+03 4.7375e+03 4.7380e+03] INFO 2025-06-26 16:55:43,049 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.28804089e+09 1.28804089e+09 1.28804089e+09 ... 1.28804562e+09 1.28804562e+09 1.28804562e+09] INFO 2025-06-26 16:55:43,049 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1288040885.2 1288040885.7, ..., timestampArray[-2:] = 1288045622.7 1288045623.2] INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1288040885.1938603), np.float64(1288040885.6938603)], ..., timestampList[-2:] = [np.float64(1288045622.6938603), np.float64(1288045623.1938603)]] INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 8818) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [8777, 8798] INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 419 INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 8818 INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1288040885.1938603), np.float64(1288040885.6938603)], ..., timestampList[-2:] = [np.float64(1288045622.6938603), np.float64(1288045623.1938603)]] INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 8818) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(8776), np.int32(8797)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 419 INFO 2025-06-26 16:55:43,059 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 419 INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1288041223.1938603)], ..., tsList[-2:] = [np.float64(1288045602.6938603), np.float64(1288045613.1938603)] INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2010-10-25 21:13:43 Z INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2010-10-25 22:26:53 Z INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 419 INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.28804529e+09], ..., cFrameEsecsList[-2:] = [1.28804529e+09 1.28804529e+09] INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2010-10-25 22:21:31 Z INFO 2025-06-26 16:55:43,068 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2010-10-25 22:21:31 Z INFO 2025-06-26 16:55:43,072 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2010.298.01/lopc.nc INFO 2025-06-26 16:55:43,072 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 16:55:43 2025 Elapsed processing time from start of processing = 7 seconds INFO 2025-06-26 16:55:43,074 process.py calibrate():227 [1] Calibration steps for 2010.298.01 INFO 2025-06-26 16:55:43,476 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 16:55:43,478 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 16:55:44,324 calibrate.py _nudge_pos():1806 [1] 124: 0.200 0.0001893 -0.0003377 1611 5.51 5.096 -11.357 2010-10-25T21:15:31.463288832 INFO 2025-06-26 16:55:46,186 calibrate.py _nudge_pos():1806 [1] 313: 0.200 -0.0005657 -0.0002269 3229 10.86 -7.725 -3.871 2010-10-25T21:29:31.465744640 INFO 2025-06-26 16:55:48,186 calibrate.py _nudge_pos():1806 [1] 517: 0.010 -0.0012913 -0.0002774 6871 23.00 -8.326 -2.235 2010-10-25T21:55:55.667219456 INFO 2025-06-26 16:55:49,588 calibrate.py _nudge_pos():1806 [1] 659: 0.010 -0.0017156 -0.0003300 9443 31.55 -8.062 -1.938 2010-10-25T22:29:49.667880704 INFO 2025-06-26 16:55:49,891 calibrate.py _nudge_pos():1806 [1] 690: 0.010 0.0000039 0.0000073 20 0.06 9.079 21.462 2010-10-25T22:30:23.665551872 INFO 2025-06-26 16:55:50,020 calibrate.py _nudge_pos():1806 [1] 703: 0.020 0.0000233 -0.0003686 1508 5.03 0.687 -13.578 2010-10-25T22:35:37.664041472 INFO 2025-06-26 16:55:50,306 calibrate.py _nudge_pos():1806 [1] 732: 0.020 0.0000079 -0.0000212 60 0.20 5.935 -19.930 2010-10-25T22:36:17.661301248 INFO 2025-06-26 16:55:51,156 calibrate.py _nudge_pos():1806 [1] 818: 0.020 -0.0017784 -0.0003380 10965 36.61 -7.198 -1.711 2010-10-25T23:14:19.664973568 INFO 2025-06-26 16:55:52,835 calibrate.py _nudge_pos():1806 [1] 986: 0.030 -0.0014927 -0.0003067 10876 36.31 -6.089 -1.565 2010-10-25T23:53:25.664261632 INFO 2025-06-26 16:55:54,389 calibrate.py _nudge_pos():1806 [1] 1142: 0.030 0.0001540 -0.0001326 1799 6.01 3.794 -4.087 2010-10-26T00:02:01.668912896 INFO 2025-06-26 16:55:55,624 calibrate.py _nudge_pos():1806 [1] 1266: 0.030 0.0016589 -0.0040932 7652 25.55 9.620 -29.690 2010-10-26T00:29:37.665469440 INFO 2025-06-26 16:55:57,011 calibrate.py _nudge_pos():1806 [1] 1403: 0.030 0.0038234 0.0004167 11000 36.73 15.426 2.102 2010-10-26T01:08:37.665168384 INFO 2025-06-26 16:55:58,064 calibrate.py _nudge_pos():1806 [1] 1507: 0.040 -0.0000015 0.0000120 55 0.18 -1.250 12.359 2010-10-26T01:10:32.667290112 INFO 2025-06-26 16:55:58,216 calibrate.py _nudge_pos():1806 [1] 1522: 0.040 0.0000204 0.0000056 15 0.05 64.925 22.402 2010-10-26T01:10:49.666125568 INFO 2025-06-26 16:55:58,227 calibrate.py _nudge_pos():1806 [1] 1523: 0.040 0.0039798 0.0003917 11145 37.20 15.861 1.951 2010-10-26T01:48:01.663223296 INFO 2025-06-26 16:55:59,619 calibrate.py _nudge_pos():1806 [1] 1660: 0.060 0.0039470 0.0003113 10800 36.03 16.244 1.601 2010-10-26T02:26:19.665799424 INFO 2025-06-26 16:56:00,921 calibrate.py _nudge_pos():1806 [1] 1786: 0.060 0.0004161 -0.0001973 2553 8.51 7.248 -4.295 2010-10-26T02:36:55.662230784 INFO 2025-06-26 16:56:01,511 calibrate.py _nudge_pos():1806 [1] 1843: 0.060 0.0034687 0.0002605 8465 28.26 18.203 1.708 2010-10-26T03:06:07.662210560 INFO 2025-06-26 16:56:02,615 calibrate.py _nudge_pos():1806 [1] 1950: 0.050 0.0000282 0.0001719 35 0.11 36.960 281.115 2010-10-26T03:08:00.664469248 INFO 2025-06-26 16:56:02,805 calibrate.py _nudge_pos():1806 [1] 1968: 0.060 0.0051428 0.0003695 11369 37.93 20.116 1.805 2010-10-26T03:46:13.667387648 INFO 2025-06-26 16:56:02,929 calibrate.py _nudge_pos():1806 [1] 1980: 0.060 0.0000246 0.0000105 30 0.10 37.764 20.097 2010-10-26T03:46:30.666223360 INFO 2025-06-26 16:56:03,573 calibrate.py _nudge_pos():1806 [1] 2042: 0.060 -0.0000019 0.0000112 15 0.05 -5.939 44.628 2010-10-26T03:47:34.661839360 INFO 2025-06-26 16:56:03,977 calibrate.py _nudge_pos():1806 [1] 2081: 0.050 0.0000880 -0.0000068 30 0.10 135.007 -13.023 2010-10-26T03:48:18.668824576 INFO 2025-06-26 16:56:04,217 calibrate.py _nudge_pos():1806 [1] 2104: 0.070 0.0066425 -0.0012596 11308 37.75 26.117 -6.184 2010-10-26T04:26:25.662155008 INFO 2025-06-26 16:56:05,577 calibrate.py _nudge_pos():1806 [1] 2236: 0.060 0.0060411 -0.0027093 11218 37.41 23.973 -13.419 2010-10-26T05:06:01.669387008 INFO 2025-06-26 16:56:06,429 calibrate.py _nudge_pos():1806 [1] 2318: 0.070 -0.0000159 -0.0000154 30 0.10 -24.391 -29.591 2010-10-26T05:07:28.663427584 INFO 2025-06-26 16:56:06,948 calibrate.py _nudge_pos():1806 [1] 2368: 0.070 0.0066221 -0.0006802 11060 36.93 26.633 -3.413 2010-10-26T05:45:13.668264192 INFO 2025-06-26 16:56:08,288 calibrate.py _nudge_pos():1806 [1] 2496: 0.070 0.0074772 -0.0016041 11110 37.08 29.962 -8.016 2010-10-26T06:24:25.667141120 INFO 2025-06-26 16:56:09,184 calibrate.py _nudge_pos():1806 [1] 2581: 0.070 -0.0000178 -0.0000102 40 0.13 -20.278 -14.535 2010-10-26T06:25:57.670838528 INFO 2025-06-26 16:56:09,537 calibrate.py _nudge_pos():1806 [1] 2615: 0.070 0.0000654 0.0000329 35 0.11 85.692 53.848 2010-10-26T06:26:37.668098816 INFO 2025-06-26 16:56:09,558 calibrate.py _nudge_pos():1806 [1] 2617: 0.080 0.0017153 -0.0021218 4134 13.78 18.498 -28.532 2010-10-26T06:40:25.661377280 INFO 2025-06-26 16:56:10,841 calibrate.py _nudge_pos():1806 [1] 2739: 0.070 0.0000431 0.0000262 20 0.06 101.166 76.755 2010-10-26T06:42:30.662813952 INFO 2025-06-26 16:56:10,853 calibrate.py _nudge_pos():1806 [1] 2740: 0.080 0.0000300 -0.0001389 3481 11.61 0.383 -2.216 2010-10-26T06:54:07.665065984 INFO 2025-06-26 16:56:12,002 calibrate.py _nudge_pos():1806 [1] 2850: 0.080 -0.0000350 -0.0000315 30 0.10 -53.756 -60.466 2010-10-26T06:56:02.667187968 INFO 2025-06-26 16:56:12,255 calibrate.py _nudge_pos():1806 [1] 2874: 0.050 0.0005895 -0.0046033 7466 24.91 3.517 -34.247 2010-10-26T07:21:20.263225344 INFO 2025-06-26 16:56:12,804 calibrate.py _nudge_pos():1806 [1] 2927: 0.070 -0.0000150 0.0002807 40 0.13 -17.139 400.122 2010-10-26T07:22:19.669155840 INFO 2025-06-26 16:56:13,673 calibrate.py _nudge_pos():1806 [1] 3010: 0.090 -0.0000156 0.0000235 20 0.06 -36.664 68.652 2010-10-26T07:23:45.663264768 INFO 2025-06-26 16:56:13,684 calibrate.py _nudge_pos():1806 [1] 3011: 0.090 -0.0004083 -0.0000814 10988 36.66 -1.654 -0.411 2010-10-26T08:00:25.662554624 INFO 2025-06-26 16:56:14,925 calibrate.py _nudge_pos():1806 [1] 3130: 0.090 0.0000560 0.0000464 15 0.05 178.300 184.205 2010-10-26T08:02:26.664265472 INFO 2025-06-26 16:56:14,978 calibrate.py _nudge_pos():1806 [1] 3135: 0.100 -0.0011949 -0.0000982 10886 36.31 -4.887 -0.501 2010-10-26T08:38:49.664719616 INFO 2025-06-26 16:56:16,384 calibrate.py _nudge_pos():1806 [1] 3268: 0.090 -0.0016142 0.0000160 11322 37.80 -6.340 0.079 2010-10-26T09:18:49.670307840 INFO 2025-06-26 16:56:17,728 calibrate.py _nudge_pos():1806 [1] 3395: 0.100 0.0024731 0.0011510 11504 38.40 9.558 5.555 2010-10-26T09:59:19.663842048 INFO 2025-06-26 16:56:18,886 calibrate.py _nudge_pos():1806 [1] 3503: 0.110 0.0021448 -0.0000941 10976 36.61 8.691 -0.476 2010-10-26T10:37:43.666007040 INFO 2025-06-26 16:56:20,258 calibrate.py _nudge_pos():1806 [1] 3631: 0.120 -0.0024937 -0.0003300 11214 37.41 -9.886 -1.635 2010-10-26T11:17:15.663514112 INFO 2025-06-26 16:56:21,729 calibrate.py _nudge_pos():1806 [1] 3768: 0.120 0.0007870 -0.0009179 11560 38.60 3.023 -4.407 2010-10-26T11:58:07.665540352 INFO 2025-06-26 16:56:22,398 calibrate.py _nudge_pos():1806 [1] 3831: 0.120 0.0000100 -0.0000185 25 0.08 18.453 -42.827 2010-10-26T11:59:14.660950784 INFO 2025-06-26 16:56:23,142 calibrate.py _nudge_pos():1806 [1] 3901: 0.120 -0.0012894 -0.0002121 11910 39.73 -4.810 -0.989 2010-10-26T12:40:07.662908672 INFO 2025-06-26 16:56:46,048 calibrate.py _nudge_pos():1862 [1] 5978: - - - 3 0.01 - - INFO 2025-06-26 16:56:46,048 calibrate.py _nudge_pos():1868 [1] Points in final series = 289239 WARNING 2025-06-26 16:56:46,528 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 16:57:15,353 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 20 of 231869 INFO 2025-06-26 16:57:17,103 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 12 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:57:33,536 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:57:35,269 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:57:35,273 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.298.01/ctd1.nc WARNING 2025-06-26 16:57:35,274 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (9060) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 16:57:35,275 calibrate.py _range_qc_combined_nc():898 [1] Setting 9060 ctd1_salinity values to NaN INFO 2025-06-26 16:57:35,275 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 16:57:35,275 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:57:47,958 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 33 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:57:49,677 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 33 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:57:49,680 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.298.01/ctd2.nc INFO 2025-06-26 16:57:49,682 calibrate.py _range_qc_combined_nc():898 [1] Setting 17 ctd2_salinity values to NaN INFO 2025-06-26 16:57:49,682 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 16:57:49,682 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:57:49,766 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 16:57:52,415 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 120 121 122 ... 3416347 3416348 3416349] INFO 2025-06-26 16:57:52,912 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 16:58:45,957 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.298.01 INFO 2025-06-26 16:58:46,178 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_cal.nc INFO 2025-06-26 16:59:11,588 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 16:59:11,596 process.py align():251 [1] Alignment steps for 2010.298.01 INFO 2025-06-26 16:59:11,690 align.py process_cal():139 [1] Processing dorado_2010.298.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.298.01 INFO 2025-06-26 16:59:11,769 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:59:11,777 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:59:11,960 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:59:11,971 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:59:12,151 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:59:12,164 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:59:12,270 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 16:59:12,271 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 16:59:12,340 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:59:12,351 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:59:12,527 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:12,537 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:59:12,692 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:12,701 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:59:12,857 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:12,866 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:59:13,020 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:13,030 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:13,191 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:13,200 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:13,357 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:13,366 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:13,523 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:13,532 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:13,687 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:13,697 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:13,851 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:13,860 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:14,015 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:14,026 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:14,183 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:14,192 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:14,349 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:14,358 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:14,516 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:14,525 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:14,680 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:14,689 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:14,848 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:14,857 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:15,017 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:15,026 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:15,183 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:15,193 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:15,351 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:15,360 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:15,518 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:15,529 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:15,684 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:15,693 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:15,851 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:15,860 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:16,016 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:59:16,025 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:59:16,216 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:59:16,334 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:59:16,458 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:59:16,583 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:59:16,720 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:59:16,967 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.95 INFO 2025-06-26 16:59:18,546 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:59:18,652 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:59:18,759 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:59:18,863 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:59:18,969 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:59:19,082 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:59:19,202 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_align.nc INFO 2025-06-26 16:59:19,540 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 16:59:19,548 process.py resample():273 [1] Resampling steps for 2010.298.01 INFO 2025-06-26 16:59:19,549 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 16:59:19,634 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_align.nc mission netCDF file INFO 2025-06-26 16:59:19,643 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_align.nc mission netCDF file INFO 2025-06-26 16:59:19,645 resample.py get_mission_start_end():1145 [1] navigation: 2010-10-25T21:08:49.050855936 to 2010-10-26T13:15:36.267089408 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 16:59:19,648 resample.py get_mission_start_end():1145 [1] hs2 : 2010-10-25T21:08:17.313029888 to 2010-10-26T13:15:36.307086592 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:59:19,650 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-10-25T21:08:34.251869696 to 2010-10-26T13:15:36.297087488 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 16:59:19,653 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-10-25T21:08:38.481580032 to 2010-10-26T13:15:36.207093504 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 16:59:19,655 resample.py get_mission_start_end():1145 [1] isus : 2010-10-25T21:09:17.428911872 to 2010-10-26T13:15:35.757124352 (0 days 00:00:00.549962240 before mission_end) INFO 2025-06-26 16:59:19,656 resample.py get_mission_start_end():1145 [1] biolume : 2010-10-25T21:08:01.564074752 to 2010-10-26T13:15:35.447111424 (0 days 00:00:00.859975168 before mission_end) INFO 2025-06-26 16:59:19,658 resample.py get_mission_start_end():1145 [1] lopc : 2010-10-25T21:13:43.193860352 to 2010-10-25T22:26:53.193860352 (0 days 14:48:43.113226240 before mission_end) WARNING 2025-06-26 16:59:19,658 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 14:48:43.113226240 INFO 2025-06-26 16:59:19,660 resample.py get_mission_start_end():1145 [1] tailcone : 2010-10-25T21:08:00.214201344 to 2010-10-26T13:15:36.227092224 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 16:59:19,661 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_align.nc mission netCDF file INFO 2025-06-26 16:59:19,662 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,271 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,368 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,470 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,562 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,641 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,729 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,810 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,888 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:20,961 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,058 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,132 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,205 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,278 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,351 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,424 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,498 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,570 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,647 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,727 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,810 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,887 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:21,965 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,043 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,119 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,150 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,180 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,204 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,229 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,254 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:22,262 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 16:59:22,262 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 16:59:24,545 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 16:59:25,343 resample.py add_biolume_proxies():633 [1] Zero flow values found: 58055 of 58055 - replaced with 350 ml/s INFO 2025-06-26 16:59:25,343 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 16:59:25,593 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 16:59:25,686 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 16:59:25,756 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 16:59:25,756 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 16:59:25,790 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:25,790 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 14:48:43.113226240 of NaNs to the end of mission INFO 2025-06-26 16:59:25,802 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:25,803 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 14:48:43.113226240 of NaNs to the end of mission INFO 2025-06-26 16:59:25,814 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:25,814 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 14:48:43.113226240 of NaNs to the end of mission INFO 2025-06-26 16:59:25,826 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:25,826 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 14:48:43.113226240 of NaNs to the end of mission INFO 2025-06-26 16:59:25,837 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:25,837 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 14:48:43.113226240 of NaNs to the end of mission INFO 2025-06-26 16:59:25,919 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 16:59:26,385 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_1S.nc INFO 2025-06-26 16:59:29,267 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 16:59:38,289 create_products.py gulper_odv():522 [1] Wrote 8 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.298.01/dorado_2010.298.01_1S_Gulper.txt INFO 2025-06-26 16:59:38,289 process.py archive():337 [1] Archiving steps for 2010.298.01 INFO 2025-06-26 16:59:38,289 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01, BASE_PATH = /data/auv_data INFO 2025-06-26 16:59:38,290 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 16:59:38,291 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.298.01_1S.nc INFO 2025-06-26 16:59:38,349 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:59:38,350 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.298.01_cal.nc INFO 2025-06-26 16:59:38,694 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:59:38,695 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.298.01_align.nc INFO 2025-06-26 16:59:39,178 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:59:39,240 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,298 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,304 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,359 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,530 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,539 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,613 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,661 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,821 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,841 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010298/2010.298.01 done. INFO 2025-06-26 16:59:39,841 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 16:59:39,843 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.298.01_1S_Gulper.txt INFO 2025-06-26 16:59:39,848 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.298.01/dorado_2010.298.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 16:59:39,848 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.298.01/dorado_2010.298.01_processing.log /Volumes/AUVCTD/surveys/2010/netcdf