INFO 2025-06-26 14:15:55,991 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 14:15:55,991 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - North bay shelf survey - ctdToUse = ctd2 INFO 2025-06-26 14:15:55,991 process.py process_mission():449 [1] Processing AUVCTD mission 2008.287.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:15:55,991 process.py download_process():165 [1] Download and processing steps for 2008.287.05 INFO 2025-06-26 14:15:55,991 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008287/2008.287.05 INFO 2025-06-26 14:15:55,991 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008287/2008.287.05 to /data/auv_data/dorado/missionlogs/2008.287.05 INFO 2025-06-26 14:16:01,844 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.287.05 INFO 2025-06-26 14:16:01,844 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/ctdDriver.log (20048116 bytes) INFO 2025-06-26 14:16:03,304 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.287.05/ctdDriver.log: [ 67191 96559 116722 195365] INFO 2025-06-26 14:16:03,365 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/ctdDriver2.log (20048197 bytes) INFO 2025-06-26 14:16:04,876 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.287.05/ctdDriver2.log: [ 7945 47150 52687 131396 223864] INFO 2025-06-26 14:16:04,941 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/gps.log (286268 bytes) INFO 2025-06-26 14:16:04,979 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/hydroscatlog.log (19147990 bytes) INFO 2025-06-26 14:16:06,960 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/navigation.log (67244314 bytes) INFO 2025-06-26 14:16:11,767 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/isuslog.log (1328053 bytes) INFO 2025-06-26 14:16:11,894 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.287.05/isuslog.log: [1 2 3 4 5 7 8] INFO 2025-06-26 14:16:11,897 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/parosci.log (23359958 bytes) INFO 2025-06-26 14:16:13,862 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/tailCone.log (2783707 bytes) INFO 2025-06-26 14:16:14,215 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/biolume.log (15513660 bytes) INFO 2025-06-26 14:16:15,715 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:16:16,492 logs2netcdfs.py download_process_logs():807 [1] Time to process: 14.65 seconds INFO 2025-06-26 14:16:16,492 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2008.287.05/lopc.bin (35034023 bytes) INFO 2025-06-26 14:16:16,493 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:16:16 2025 INFO 2025-06-26 14:16:16,493 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.287.05/parosci.nc INFO 2025-06-26 14:16:16,493 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:16:16,493 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.287.05/parosci.nc INFO 2025-06-26 14:16:16,496 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1223937955.3, sensor_off_time = 1223994968.7 INFO 2025-06-26 14:16:16,496 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 57013 seconds. Expecting to read 114026 L frames from the lopc.bin file. INFO 2025-06-26 14:16:16,497 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 114026 records from the lopc.bin file. INFO 2025-06-26 14:16:17,170 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2008-10-13 22:45:55 Z and endTime = 2008-10-14 14:36:08 Z with 114026 records expected to be read from lopc.bin INFO 2025-06-26 14:16:17,170 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2008.287.05/lopc.bin INFO 2025-06-26 14:16:17,170 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2008.287.05/lopc.nc INFO 2025-06-26 14:16:17,171 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2008.287.05/lopc.nc INFO 2025-06-26 14:16:17,171 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2008.287.05 INFO 2025-06-26 14:16:17,171 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 14:16:17,251 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x84 in position 0: invalid start byte INFO 2025-06-26 14:16:17,251 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 14:16:17,251 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.287.05/parosci.nc INFO 2025-06-26 14:16:17,251 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:16:17,251 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.287.05/parosci.nc INFO 2025-06-26 14:16:17,254 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1223937955.3, sensor_off_time = 1223994968.7 INFO 2025-06-26 14:16:17,254 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 57013 seconds. Expecting to read 114026 L frames from the lopc.bin file. INFO 2025-06-26 14:16:17,254 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 114026 records from the lopc.bin file. INFO 2025-06-26 14:16:17,254 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 21145 and len(sampleCountList) = 87 INFO 2025-06-26 14:16:17,254 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 14:16:17,255 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [21145 21146 21147 21148 21149 21150 21151 21152 21153 21154 21155 21156 21157 21158 21159 21165 21166 21167 21168 21169 21170 21171 21172 21173 21174 21175 21176 21177 21182 21183 21184 21185 21186 21187 21188 21189 21190 21191 21192 21193 21194 21195 21203 21204 21205 21206 21207 21208 21217 21218 21219 21220 21221 21222 21223 21224 21225 21233 21234 21235 21236 21237 21238 21239 21240 21241 21248 21249 21250 21251 21252 21261 21262 21263 21264 21265 21266 21381 21276 21277 21287 21288 21289 21290 21291 21302 21303] INFO 2025-06-26 14:16:17,255 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 14:16:17,255 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 14:16:17,255 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 8 1 1 1 1 1 9 1 1 1 1 1 1 1 1 8 1 1 1 1 1 1 1 1 7 1 1 1 1 9 1 1 1 1 1 115 -105 1 10 1 1 1 1 11 1] INFO 2025-06-26 14:16:17,256 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 14:16:17,256 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [21145 21146 21147 21148 21149 21150 21151 21152 21153 21154 21155 21156 21157 21158 21159 21165 21166 21167 21168 21169 21170 21171 21172 21173 21174 21175 21176 21177 21182 21183 21184 21185 21186 21187 21188 21189 21190 21191 21192 21193 21194 21195 21203 21204 21205 21206 21207 21208 21217 21218 21219 21220 21221 21222 21223 21224 21225 21233 21234 21235 21236 21237 21238 21239 21240 21241 21248 21249 21250 21251 21252 21261 21262 21263 21264 21265 21266 21381 21276 21277 21287 21288 21289 21290 21291 21302 21303] INFO 2025-06-26 14:16:17,256 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [21145 21146 21147 21148 21149 21150 21151 21152 21153 21154 21155 21156 21157 21158 21159 21165 21166 21167 21168 21169 21170 21171 21172 21173 21174 21175 21176 21177 21182 21183 21184 21185 21186 21187 21188 21189 21190 21191 21192 21193 21194 21195 21203 21204 21205 21206 21207 21208 21217 21218 21219 21220 21221 21222 21223 21224 21225 21233 21234 21235 21236 21237 21238 21239 21240 21241 21248 21249 21250 21251 21252 21261 21262 21263 21264 21265 21266 21381 21276 21277 21287 21288 21289 21290 21291 21302 21303] with len(correctedSampleCountList) = 87 INFO 2025-06-26 14:16:17,256 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 21145 from all values of correctedSampleCountList INFO 2025-06-26 14:16:17,256 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 14:16:17,256 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [ 0. 0.5 1. 1.5 2. 2.5 3. 3.5 4. 4.5 5. 5.5 6. 6.5 7. 10. 10.5 11. 11.5 12. 12.5 13. 13.5 14. 14.5 15. 15.5 16. 18.5 19. 19.5 20. 20.5 21. 21.5 22. 22.5 23. 23.5 24. 24.5 25. 29. 29.5 30. 30.5 31. 31.5 36. 36.5 37. 37.5 38. 38.5 39. 39.5 40. 44. 44.5 45. 45.5 46. 46.5 47. 47.5 48. 51.5 52. 52.5 53. 53.5 58. 58.5 59. 59.5 60. 60.5 118. 65.5 66. 71. 71.5 72. 72.5 73. 78.5 79. ] INFO 2025-06-26 14:16:17,257 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393796e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393797e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393798e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393799e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393800e+09 1.22393801e+09 1.22393801e+09 1.22393801e+09 1.22393801e+09 1.22393801e+09 1.22393801e+09 1.22393801e+09 1.22393801e+09 1.22393801e+09 1.22393802e+09 1.22393802e+09 1.22393807e+09 1.22393802e+09 1.22393802e+09 1.22393803e+09 1.22393803e+09 1.22393803e+09 1.22393803e+09 1.22393803e+09 1.22393803e+09 1.22393803e+09] INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1223937955.3 1223937955.8, ..., timestampArray[-2:] = 1223938033.8 1223938034.3] INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1223937955.3199646), np.float64(1223937955.8199646)], ..., timestampList[-2:] = [np.float64(1223938033.8199646), np.float64(1223938034.3199646)]] INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 87) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [62, 83] INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 4 INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 87 INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1223937955.3199646), np.float64(1223937955.8199646)], ..., timestampList[-2:] = [np.float64(1223938033.8199646), np.float64(1223938034.3199646)]] INFO 2025-06-26 14:16:17,258 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 87) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:16:17,259 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(61), np.int32(82)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 14:16:17,259 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 4 INFO 2025-06-26 14:16:17,259 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 14:16:17,259 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 4 INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1223937967.3199646)], ..., tsList[-2:] = [np.float64(1223938001.3199646), np.float64(1223938027.3199646)] INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2008-10-13 22:46:07 Z INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2008-10-13 22:47:07 Z INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 86 INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:16:17,260 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:16:17,264 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2008.287.05/lopc.nc INFO 2025-06-26 14:16:17,264 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 14:16:17 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 14:16:17,265 process.py calibrate():227 [1] Calibration steps for 2008.287.05 INFO 2025-06-26 14:16:17,649 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 14:16:17,651 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:16:18,336 calibrate.py _nudge_pos():1806 [1] 94: 0.150 -0.0000695 0.0000200 2440 8.13 -1.269 0.456 2008-10-13T22:55:30.250579456 INFO 2025-06-26 14:16:19,056 calibrate.py _nudge_pos():1806 [1] 167: 0.150 0.0000376 -0.0000331 5065 16.88 0.331 -0.363 2008-10-13T23:13:35.256251392 INFO 2025-06-26 14:16:19,439 calibrate.py _nudge_pos():1806 [1] 206: 0.170 -0.0000323 0.0000012 2210 7.36 -0.650 0.031 2008-10-13T23:21:35.253369344 INFO 2025-06-26 14:16:19,901 calibrate.py _nudge_pos():1806 [1] 253: 0.160 0.0000572 0.0002951 4030 13.43 0.632 4.072 2008-10-13T23:35:47.255003136 INFO 2025-06-26 14:16:20,313 calibrate.py _nudge_pos():1806 [1] 294: 0.160 -0.0000048 0.0000058 2140 7.13 -0.100 0.149 2008-10-13T23:43:35.252943104 INFO 2025-06-26 14:16:20,774 calibrate.py _nudge_pos():1806 [1] 341: 0.160 0.0000754 -0.0000215 5350 17.83 0.627 -0.223 2008-10-14T00:02:11.256491776 INFO 2025-06-26 14:16:21,248 calibrate.py _nudge_pos():1806 [1] 389: 0.170 0.0001727 0.0000583 9215 30.71 0.834 0.352 2008-10-14T00:33:41.257017600 INFO 2025-06-26 14:16:21,810 calibrate.py _nudge_pos():1806 [1] 445: 0.170 0.0001117 0.0000324 9355 31.18 0.531 0.192 2008-10-14T01:05:47.255077888 INFO 2025-06-26 14:16:22,191 calibrate.py _nudge_pos():1806 [1] 483: 0.180 0.0001895 0.0000592 9355 31.18 0.901 0.352 2008-10-14T01:37:35.254370816 INFO 2025-06-26 14:16:22,438 calibrate.py _nudge_pos():1806 [1] 508: 0.180 -0.0000068 0.0000052 25 0.08 -12.609 12.074 2008-10-14T01:38:05.252315648 INFO 2025-06-26 14:16:22,479 calibrate.py _nudge_pos():1806 [1] 512: 0.180 0.0002684 0.0000765 9345 31.15 1.277 0.455 2008-10-14T02:09:17.254075136 INFO 2025-06-26 14:16:22,929 calibrate.py _nudge_pos():1806 [1] 556: 0.180 0.0001491 0.0000611 7885 26.28 0.840 0.431 2008-10-14T02:36:17.253097472 INFO 2025-06-26 14:16:23,101 calibrate.py _nudge_pos():1806 [1] 573: 0.180 -0.0000039 -0.0000773 75 0.25 -2.321 -58.065 2008-10-14T02:36:48.250973952 INFO 2025-06-26 14:16:23,161 calibrate.py _nudge_pos():1806 [1] 579: 0.190 -0.0000147 0.0000456 25 0.08 -27.208 105.521 2008-10-14T02:36:58.250288896 INFO 2025-06-26 14:16:23,212 calibrate.py _nudge_pos():1806 [1] 584: 0.190 -0.0000024 0.0000138 15 0.05 -7.632 54.880 2008-10-14T02:37:05.249809408 INFO 2025-06-26 14:16:23,352 calibrate.py _nudge_pos():1806 [1] 598: 0.180 0.0000139 0.0002682 4615 15.38 0.133 3.231 2008-10-14T02:52:41.255688704 INFO 2025-06-26 14:16:23,861 calibrate.py _nudge_pos():1806 [1] 649: 0.190 0.0010919 0.0001010 2360 7.86 20.570 2.380 2008-10-14T03:01:23.249929728 INFO 2025-06-26 14:16:24,204 calibrate.py _nudge_pos():1806 [1] 683: 0.180 -0.0000396 0.0000170 15 0.05 -125.624 67.638 2008-10-14T03:01:59.257463040 INFO 2025-06-26 14:16:24,245 calibrate.py _nudge_pos():1806 [1] 687: 0.190 0.0001216 0.0000717 4605 15.35 1.173 0.866 2008-10-14T03:17:23.254164736 INFO 2025-06-26 14:16:24,667 calibrate.py _nudge_pos():1806 [1] 729: 0.200 0.0009700 0.0000595 2345 7.81 18.392 1.412 2008-10-14T03:25:53.249227776 INFO 2025-06-26 14:16:25,086 calibrate.py _nudge_pos():1806 [1] 770: 0.190 0.0000102 0.0002609 4390 14.63 0.103 3.305 2008-10-14T03:41:11.256339968 INFO 2025-06-26 14:16:25,457 calibrate.py _nudge_pos():1806 [1] 807: 0.200 0.0032855 0.0018199 9329 31.09 15.657 10.846 2008-10-14T04:12:53.256044032 INFO 2025-06-26 14:16:25,861 calibrate.py _nudge_pos():1806 [1] 847: 0.200 0.0044975 0.0021424 11592 38.64 17.250 10.273 2008-10-14T04:52:11.254510080 INFO 2025-06-26 14:16:25,883 calibrate.py _nudge_pos():1806 [1] 849: 0.200 0.0000229 -0.0000022 94 0.31 10.937 -1.323 2008-10-14T04:52:31.253139968 INFO 2025-06-26 14:16:26,245 calibrate.py _nudge_pos():1806 [1] 884: 0.010 0.0049266 0.0020971 11550 38.50 18.974 10.094 2008-10-14T05:31:35.452551424 INFO 2025-06-26 14:16:26,340 calibrate.py _nudge_pos():1806 [1] 893: 0.010 -0.0000081 0.0001342 135 0.45 -2.674 55.668 2008-10-14T05:32:10.450153728 INFO 2025-06-26 14:16:26,700 calibrate.py _nudge_pos():1806 [1] 928: 0.010 0.0046136 0.0018308 10695 35.65 19.195 9.517 2008-10-14T06:08:23.451293184 INFO 2025-06-26 14:16:27,106 calibrate.py _nudge_pos():1806 [1] 967: 0.010 0.0013459 0.0003105 3110 10.36 19.263 5.551 2008-10-14T06:19:23.456079616 INFO 2025-06-26 14:16:27,603 calibrate.py _nudge_pos():1806 [1] 1015: 0.020 0.0000053 0.0000521 5075 16.91 0.047 0.570 2008-10-14T06:37:05.453327872 INFO 2025-06-26 14:16:28,014 calibrate.py _nudge_pos():1806 [1] 1054: 0.020 -0.0000738 0.0000057 2330 7.76 -1.411 0.136 2008-10-14T06:45:29.448801792 INFO 2025-06-26 14:16:28,445 calibrate.py _nudge_pos():1806 [1] 1095: 0.030 0.0000403 0.0002841 4840 16.13 0.370 3.264 2008-10-14T07:02:17.449748992 INFO 2025-06-26 14:16:28,825 calibrate.py _nudge_pos():1806 [1] 1132: 0.020 0.0000391 0.0000070 2190 7.30 0.796 0.178 2008-10-14T07:10:11.457277184 INFO 2025-06-26 14:16:29,164 calibrate.py _nudge_pos():1806 [1] 1164: 0.020 0.0000678 -0.0000500 4225 14.08 0.714 -0.658 2008-10-14T07:24:47.457267200 INFO 2025-06-26 14:16:29,525 calibrate.py _nudge_pos():1806 [1] 1199: 0.030 0.0001914 0.0000497 9640 32.13 0.883 0.286 2008-10-14T07:57:29.452861184 INFO 2025-06-26 14:16:30,123 calibrate.py _nudge_pos():1806 [1] 1256: 0.040 0.0001891 0.0000901 9500 31.66 0.885 0.527 2008-10-14T08:30:05.448866304 INFO 2025-06-26 14:16:30,776 calibrate.py _nudge_pos():1806 [1] 1314: 0.040 0.0002464 0.0000751 9704 32.35 1.129 0.430 2008-10-14T09:03:23.451993600 INFO 2025-06-26 14:16:31,387 calibrate.py _nudge_pos():1806 [1] 1373: 0.040 0.0002069 0.0001172 9519 31.73 0.966 0.684 2008-10-14T09:36:05.457587200 INFO 2025-06-26 14:16:31,963 calibrate.py _nudge_pos():1806 [1] 1429: 0.050 0.0001359 0.0000238 7375 24.58 0.819 0.179 2008-10-14T10:01:35.452775424 INFO 2025-06-26 14:16:32,338 calibrate.py _nudge_pos():1806 [1] 1465: 0.050 0.0000168 0.0002970 4535 15.11 0.165 3.641 2008-10-14T10:17:17.448244224 INFO 2025-06-26 14:16:32,725 calibrate.py _nudge_pos():1806 [1] 1502: 0.050 0.0010902 0.0000290 2520 8.40 19.233 0.641 2008-10-14T10:26:17.451251456 INFO 2025-06-26 14:16:33,089 calibrate.py _nudge_pos():1806 [1] 1536: 0.040 0.0000057 0.0000525 2470 8.23 0.102 1.183 2008-10-14T10:35:05.455080704 INFO 2025-06-26 14:16:33,163 calibrate.py _nudge_pos():1806 [1] 1542: 0.050 0.0000716 0.0000676 2195 7.31 1.451 1.713 2008-10-14T10:42:29.454664704 INFO 2025-06-26 14:16:33,516 calibrate.py _nudge_pos():1806 [1] 1576: 0.050 0.0009550 0.0000930 2235 7.45 18.998 2.313 2008-10-14T10:50:29.451782656 INFO 2025-06-26 14:16:33,659 calibrate.py _nudge_pos():1806 [1] 1589: 0.050 -0.0000095 -0.0000158 15 0.05 -30.225 -62.606 2008-10-14T10:50:45.450686720 INFO 2025-06-26 14:16:33,997 calibrate.py _nudge_pos():1806 [1] 1621: 0.060 -0.0000227 0.0002920 4325 14.41 -0.233 3.754 2008-10-14T11:05:41.449306368 INFO 2025-06-26 14:16:34,372 calibrate.py _nudge_pos():1806 [1] 1656: 0.060 0.0033856 0.0018091 9670 32.23 15.565 10.401 2008-10-14T11:38:29.454489088 INFO 2025-06-26 14:16:34,719 calibrate.py _nudge_pos():1806 [1] 1689: 0.060 0.0046042 0.0021060 12200 40.66 16.782 9.597 2008-10-14T12:19:41.455145472 INFO 2025-06-26 14:16:35,353 calibrate.py _nudge_pos():1806 [1] 1743: 0.070 0.0049849 0.0020771 11734 39.11 18.896 9.840 2008-10-14T12:59:41.450734336 INFO 2025-06-26 14:16:35,398 calibrate.py _nudge_pos():1806 [1] 1747: 0.080 -0.0000121 0.0000113 100 0.33 -5.448 6.358 2008-10-14T13:00:04.449158912 INFO 2025-06-26 14:16:35,984 calibrate.py _nudge_pos():1806 [1] 1800: 0.080 0.0049531 0.0018601 11380 37.93 19.367 9.087 2008-10-14T13:38:53.449611520 INFO 2025-06-26 14:16:36,389 calibrate.py _nudge_pos():1806 [1] 1836: 0.080 0.0001585 0.0000032 3305 11.01 2.135 0.055 2008-10-14T13:50:29.451931904 INFO 2025-06-26 14:16:36,814 calibrate.py _nudge_pos():1806 [1] 1872: 0.080 0.0007296 0.0006802 3065 10.21 10.595 12.341 2008-10-14T14:01:17.457540608 INFO 2025-06-26 14:16:59,643 calibrate.py _nudge_pos():1862 [1] 3931: - - - 1 0.00 - - INFO 2025-06-26 14:16:59,643 calibrate.py _nudge_pos():1868 [1] Points in final series = 284814 WARNING 2025-06-26 14:17:00,019 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:17:02,230 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:17:18,624 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 14 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:17:20,396 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 14 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:17:20,400 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.287.05/ctd1.nc INFO 2025-06-26 14:17:20,402 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:17:20,402 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 14:17:20,402 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:17:32,953 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 14 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:17:34,735 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 14 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:17:34,739 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.287.05/ctd2.nc INFO 2025-06-26 14:17:34,740 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 14:17:34,741 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 14:17:34,741 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:17:36,779 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:17:39,459 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 840 841 842 843 10860 10861 10862 10863 10864 10865 23580 23581 23582 23583 30420 30421 30422 30423 30424 30425 35700 35701 35702 35703 67860 67861 67862 194520 297540 297541 297542 297543 297544 297545 297546 328500 328501 328502 357900 357901 357902 357903 357904 357905 357906 523560 523561 523562 523563 599340 599341 599342 599343 626880 704760 812640 812641 954420 954421 954422 954423 1069140 1069141 1069142 1326900 1326901 1326902 1401720 1568760 1616460 1616461 1616462 1616463 1787520 1787521 1787522 1787523 1787524 1787525 1787526 1796400 1829760 1855920 1855921 2455620 2455621 2455622 2455623 2455624 2455625 2455626 2455627 2464920 2464921 2556300 2556301 2556302 2556303 2556304 2556305 2656980 2656981 2656982 2656983 2895660 2895661 2895662 2895663 3002880 3002881 3002882 3002883 3002884 3056280 3056281 3056282 3056283 3084420 3084421 3084422 3084423 3142740 3142741 3142742 3142743 3142744 3180240 3180241 3321480 3321481 3321482] INFO 2025-06-26 14:17:39,954 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:17:39,960 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 14:17:39,970 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.287.05 INFO 2025-06-26 14:17:40,020 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_cal.nc INFO 2025-06-26 14:17:57,625 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 14:17:57,632 process.py align():251 [1] Alignment steps for 2008.287.05 INFO 2025-06-26 14:17:57,676 align.py process_cal():139 [1] Processing dorado_2008.287.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.287.05 INFO 2025-06-26 14:17:57,751 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:17:57,760 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:17:57,956 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:17:57,969 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:17:58,142 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:17:58,155 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:17:58,261 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:17:58,262 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:17:58,336 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:17:58,346 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:17:58,516 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:58,525 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:58,675 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:58,684 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:58,845 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:58,853 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:59,004 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:59,013 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:59,177 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:59,185 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:59,339 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:59,348 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:59,500 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:59,508 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:59,660 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:59,669 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:59,822 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:59,831 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:17:59,981 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:17:59,991 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:00,155 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:00,163 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:00,314 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:00,323 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:00,485 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:00,493 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:00,650 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:00,659 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:00,813 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:00,821 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:00,974 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:00,983 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:01,140 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:01,148 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:01,301 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:01,311 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:01,467 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:01,476 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:01,627 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.287.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:18:01,635 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:18:01,822 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:18:01,936 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:18:02,054 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:18:02,194 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:18:02,320 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.05 INFO 2025-06-26 14:18:02,424 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.05 INFO 2025-06-26 14:18:02,528 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.05 INFO 2025-06-26 14:18:02,626 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.05 INFO 2025-06-26 14:18:02,726 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.05 INFO 2025-06-26 14:18:02,826 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 14:18:02,861 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_align.nc INFO 2025-06-26 14:18:02,991 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 14:18:02,994 process.py resample():273 [1] Resampling steps for 2008.287.05 INFO 2025-06-26 14:18:02,995 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:18:03,027 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_align.nc mission netCDF file INFO 2025-06-26 14:18:03,035 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_align.nc mission netCDF file INFO 2025-06-26 14:18:03,037 resample.py get_mission_start_end():1145 [1] navigation: 2008-10-13T22:46:22.978070016 to 2008-10-14T14:36:08.654283776 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 14:18:03,039 resample.py get_mission_start_end():1145 [1] hs2 : 2008-10-13T22:45:55.959920896 to 2008-10-14T14:36:08.634285312 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 14:18:03,042 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-10-13T22:46:09.528991232 to 2008-10-14T14:36:08.614286336 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 14:18:03,044 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-10-13T22:46:09.428998144 to 2008-10-14T14:36:08.674282240 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:18:03,046 resample.py get_mission_start_end():1145 [1] isus : 2008-10-13T22:46:50.506184192 to 2008-10-14T14:36:07.744346112 (0 days 00:00:00.929936128 before mission_end) INFO 2025-06-26 14:18:03,048 resample.py get_mission_start_end():1145 [1] biolume : 2008-10-13T22:45:50.050291456 to 2008-10-14T14:36:07.884302336 (0 days 00:00:00.789979904 before mission_end) INFO 2025-06-26 14:18:03,049 resample.py get_mission_start_end():1145 [1] lopc : 2008-10-13T22:46:07.319964672 to 2008-10-13T22:47:07.319964672 (0 days 15:49:01.354317568 before mission_end) WARNING 2025-06-26 14:18:03,050 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 15:49:01.354317568 INFO 2025-06-26 14:18:03,051 resample.py get_mission_start_end():1145 [1] tailcone : 2008-10-13T22:45:54.620012800 to 2008-10-14T14:36:08.324306432 (0 days 00:00:00.349975808 before mission_end) INFO 2025-06-26 14:18:03,052 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_align.nc mission netCDF file INFO 2025-06-26 14:18:03,052 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:03,636 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:03,728 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:03,819 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:03,908 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:03,985 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,062 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,136 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,210 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,283 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,354 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,425 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,496 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,567 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,638 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,710 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,783 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,857 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:04,935 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,009 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,084 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,158 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,232 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,261 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,286 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,310 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,338 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,352 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,352 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 15:49:01.354317568 of NaNs to the end of mission INFO 2025-06-26 14:18:05,364 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,364 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 15:49:01.354317568 of NaNs to the end of mission INFO 2025-06-26 14:18:05,374 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,374 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 15:49:01.354317568 of NaNs to the end of mission INFO 2025-06-26 14:18:05,384 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,384 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 15:49:01.354317568 of NaNs to the end of mission INFO 2025-06-26 14:18:05,394 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,394 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 15:49:01.354317568 of NaNs to the end of mission INFO 2025-06-26 14:18:05,419 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:18:05,844 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_1S.nc INFO 2025-06-26 14:18:08,964 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 14:18:18,793 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.287.05/dorado_2008.287.05_1S_Gulper.txt INFO 2025-06-26 14:18:18,794 process.py archive():337 [1] Archiving steps for 2008.287.05 INFO 2025-06-26 14:18:18,794 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05, BASE_PATH = /data/auv_data INFO 2025-06-26 14:18:18,795 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 14:18:18,796 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.287.05_1S.nc INFO 2025-06-26 14:18:18,838 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:18:18,839 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.287.05_cal.nc INFO 2025-06-26 14:18:19,036 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:18:19,037 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.287.05_align.nc INFO 2025-06-26 14:18:19,225 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:18:19,280 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,334 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,340 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,393 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,576 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,585 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,653 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,668 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,831 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,837 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008287/2008.287.05 done. INFO 2025-06-26 14:18:19,837 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:18:19,838 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.287.05_1S_Gulper.txt INFO 2025-06-26 14:18:19,842 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.287.05/dorado_2008.287.05_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 14:18:19,843 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.287.05/dorado_2008.287.05_processing.log /Volumes/AUVCTD/surveys/2008/netcdf