INFO 2025-06-26 19:27:48,732 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 19:27:48,732 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ECOHAB - CANON March 2013 - drifter tracking T-REX mission, 2 Gulpers on .05 , 8 Gulpers on .06 - stitched together - ctdToUse = ctd1 INFO 2025-06-26 19:27:48,732 process.py process_mission():449 [1] Processing CANON March 2013 mission 2013.075.06 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:27:48,732 process.py download_process():165 [1] Download and processing steps for 2013.075.06 INFO 2025-06-26 19:27:48,732 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013075/2013.075.06 INFO 2025-06-26 19:27:48,732 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013075/2013.075.06 to /data/auv_data/dorado/missionlogs/2013.075.06 INFO 2025-06-26 19:27:50,583 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.075.06 INFO 2025-06-26 19:27:50,583 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/ctdDriver.log (3594342 bytes) INFO 2025-06-26 19:27:50,846 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/ctdDriver2.log (3594143 bytes) INFO 2025-06-26 19:27:51,109 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/gps.log (151052 bytes) INFO 2025-06-26 19:27:51,132 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/hydroscatlog.log (3151366 bytes) INFO 2025-06-26 19:27:51,464 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/navigation.log (12719942 bytes) INFO 2025-06-26 19:27:52,377 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/isuslog.log (277525 bytes) INFO 2025-06-26 19:27:52,407 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/parosci.log (3813446 bytes) INFO 2025-06-26 19:27:52,733 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.15 seconds INFO 2025-06-26 19:27:52,733 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.075.06/lopc.bin (43692714 bytes) INFO 2025-06-26 19:27:52,733 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:27:52 2025 INFO 2025-06-26 19:27:52,733 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.075.06/parosci.nc INFO 2025-06-26 19:27:52,733 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:27:52,733 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.075.06/parosci.nc INFO 2025-06-26 19:27:52,736 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363458416.4, sensor_off_time = 1363467802.6 INFO 2025-06-26 19:27:52,737 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 9386 seconds. Expecting to read 18772 L frames from the lopc.bin file. INFO 2025-06-26 19:27:52,737 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 18772 records from the lopc.bin file. INFO 2025-06-26 19:27:52,846 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-03-16 18:26:56 Z and endTime = 2013-03-16 21:03:22 Z with 18772 records expected to be read from lopc.bin INFO 2025-06-26 19:27:52,846 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.075.06/lopc.bin INFO 2025-06-26 19:27:52,846 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.075.06/lopc.nc INFO 2025-06-26 19:27:52,847 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.075.06/lopc.nc INFO 2025-06-26 19:27:52,847 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.075.06 INFO 2025-06-26 19:27:52,847 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:27:52,971 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:27:52,971 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:27:52,971 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:27:54,499 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd3 in position 0: unexpected end of data INFO 2025-06-26 19:27:54,499 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 19:27:54,499 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.075.06/parosci.nc INFO 2025-06-26 19:27:54,499 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:27:54,499 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.075.06/parosci.nc INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363458416.4, sensor_off_time = 1363467802.6 INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 9386 seconds. Expecting to read 18772 L frames from the lopc.bin file. INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 18772 records from the lopc.bin file. INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 1012 INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1 2 3 ... 1010 1011 1012] INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 19:27:54,503 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 19:27:54,504 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 19:27:54,504 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1 2 3 ... 1010 1011 1012] INFO 2025-06-26 19:27:54,504 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1 2 3 ... 1010 1011 1012] with len(correctedSampleCountList) = 1012 INFO 2025-06-26 19:27:54,504 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-26 19:27:54,504 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 19:27:54,504 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.000e+00 5.000e-01 1.000e+00 ... 5.045e+02 5.050e+02 5.055e+02] INFO 2025-06-26 19:27:54,504 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.36345842e+09 1.36345842e+09 1.36345842e+09 ... 1.36345892e+09 1.36345892e+09 1.36345892e+09] INFO 2025-06-26 19:27:54,505 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1363458416.4 1363458416.9, ..., timestampArray[-2:] = 1363458921.4 1363458921.9] INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1363458416.4341855), np.float64(1363458416.9341855)], ..., timestampList[-2:] = [np.float64(1363458921.4341855), np.float64(1363458921.9341855)]] INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 1012) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [986, 1007] INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 48 INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 1012 INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1363458416.4341855), np.float64(1363458416.9341855)], ..., timestampList[-2:] = [np.float64(1363458921.4341855), np.float64(1363458921.9341855)]] INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 1012) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(985), np.int32(1006)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 48 INFO 2025-06-26 19:27:54,506 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 19:27:54,508 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 48 INFO 2025-06-26 19:27:54,508 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1363458425.9341855)], ..., tsList[-2:] = [np.float64(1363458908.9341855), np.float64(1363458919.4341855)] INFO 2025-06-26 19:27:54,508 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2013-03-16 18:27:05 Z INFO 2025-06-26 19:27:54,508 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2013-03-16 18:35:19 Z INFO 2025-06-26 19:27:54,508 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 48 INFO 2025-06-26 19:27:54,508 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.36345892e+09], ..., cFrameEsecsList[-2:] = [1.36345892e+09 1.36345892e+09] INFO 2025-06-26 19:27:54,509 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2013-03-16 18:35:18 Z INFO 2025-06-26 19:27:54,509 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2013-03-16 18:35:18 Z INFO 2025-06-26 19:27:54,512 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2013.075.06/lopc.nc INFO 2025-06-26 19:27:54,513 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 19:27:54 2025 Elapsed processing time from start of processing = 1 seconds INFO 2025-06-26 19:27:54,513 process.py calibrate():227 [1] Calibration steps for 2013.075.06 INFO 2025-06-26 19:27:54,697 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 19:27:54,699 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:27:59,310 calibrate.py _nudge_pos():1806 [1] 530: 0.160 0.0032648 -0.0010556 6324 21.08 23.903 -9.279 2013-03-16T18:56:48.041452032 INFO 2025-06-26 19:28:01,409 calibrate.py _nudge_pos():1806 [1] 757: 0.160 0.0006289 -0.0019581 6240 20.80 4.667 -17.447 2013-03-16T19:21:22.040476160 INFO 2025-06-26 19:28:02,633 calibrate.py _nudge_pos():1806 [1] 888: 0.170 -0.0003217 -0.0030988 5050 16.83 -2.950 -34.118 2013-03-16T19:40:22.032381184 INFO 2025-06-26 19:28:09,243 calibrate.py _nudge_pos():1806 [1] 1599: 0.170 0.0046673 -0.0052747 7790 25.96 27.742 -37.645 2013-03-16T20:18:10.037012224 INFO 2025-06-26 19:28:10,434 calibrate.py _nudge_pos():1806 [1] 1727: 0.180 0.0008871 -0.0044142 9145 30.48 4.491 -26.836 2013-03-16T20:50:46.033017344 INFO 2025-06-26 19:28:11,848 calibrate.py _nudge_pos():1806 [1] 1879: 0.180 0.0000241 0.0000300 1945 6.48 0.574 0.857 2013-03-16T20:59:46.036024576 INFO 2025-06-26 19:28:11,868 calibrate.py _nudge_pos():1806 [1] 1881: 0.180 0.0000138 0.0000087 55 0.18 11.829 8.990 2013-03-16T20:59:58.035202816 INFO 2025-06-26 19:28:13,786 calibrate.py _nudge_pos():1862 [1] 2049: - - - 3 0.01 - - INFO 2025-06-26 19:28:13,786 calibrate.py _nudge_pos():1868 [1] Points in final series = 46753 WARNING 2025-06-26 19:28:13,850 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:28:14,204 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:28:14,560 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:14,836 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:14,838 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.075.06/ctd1.nc INFO 2025-06-26 19:28:14,839 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:28:14,839 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 19:28:14,839 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:28:15,173 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:15,449 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:15,451 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.075.06/ctd2.nc INFO 2025-06-26 19:28:15,452 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:28:15,452 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 19:28:15,452 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:28:15,465 calibrate.py process_logs():3542 [1] Error processing biolume: biolume has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.075.06 ERROR 2025-06-26 19:28:15,474 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.075.06 ERROR 2025-06-26 19:28:15,474 calibrate.py process_logs():3542 [1] Error processing tailcone: tailcone has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.075.06 INFO 2025-06-26 19:28:15,474 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_cal.nc INFO 2025-06-26 19:28:15,536 calibrate.py write_netcdf():3512 [1] Data variables written: 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, time INFO 2025-06-26 19:28:15,542 process.py align():251 [1] Alignment steps for 2013.075.06 INFO 2025-06-26 19:28:15,567 align.py process_cal():139 [1] Processing dorado_2013.075.06_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.075.06 INFO 2025-06-26 19:28:15,583 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:15,586 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:15,623 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:15,626 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:15,662 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:15,665 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:15,686 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:28:15,687 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:28:15,701 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:15,704 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:15,739 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,742 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:15,774 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,777 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:15,810 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,813 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:15,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,848 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:15,881 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,884 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:15,916 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,919 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:15,953 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,956 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:15,988 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:15,991 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,025 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,028 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,060 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,064 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,097 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,100 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,133 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,136 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,169 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,172 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,204 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,207 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,241 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,244 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,277 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,280 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,314 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,317 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,350 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,353 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,387 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,390 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,423 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,427 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,461 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,464 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,496 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.075.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:16,499 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:16,540 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:28:16,570 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:28:16,601 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:28:16,632 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:28:16,659 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:28:16,687 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:28:16,714 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:28:16,741 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:28:16,750 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_align.nc INFO 2025-06-26 19:28:16,805 align.py write_netcdf():342 [1] Data variables written: 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 INFO 2025-06-26 19:28:16,807 process.py resample():273 [1] Resampling steps for 2013.075.06 INFO 2025-06-26 19:28:16,808 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:28:16,830 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_align.nc mission netCDF file INFO 2025-06-26 19:28:16,834 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_align.nc mission netCDF file INFO 2025-06-26 19:28:16,835 resample.py get_mission_start_end():1145 [1] navigation: 2013-03-16T18:27:31.451786496 to 2013-03-16T21:03:22.641186304 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:28:16,837 resample.py get_mission_start_end():1145 [1] hs2 : 2013-03-16T18:27:02.593763328 to 2013-03-16T21:03:22.611188224 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 19:28:16,838 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-03-16T18:27:24.422268160 to 2013-03-16T21:03:22.461198592 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 19:28:16,840 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-03-16T18:27:24.932233216 to 2013-03-16T21:03:22.441200128 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 19:28:16,841 resample.py get_mission_start_end():1145 [1] isus : 2013-03-16T18:28:11.129068288 to 2013-03-16T21:03:21.131289600 (0 days 00:00:01.509896704 before mission_end) INFO 2025-06-26 19:28:16,842 resample.py get_mission_start_end():1145 [1] lopc : 2013-03-16T18:27:05.934185472 to 2013-03-16T18:35:19.434185472 (0 days 02:28:03.207000832 before mission_end) WARNING 2025-06-26 19:28:16,843 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 02:28:03.207000832 INFO 2025-06-26 19:28:16,843 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_align.nc mission netCDF file INFO 2025-06-26 19:28:16,843 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:16,962 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:16,984 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,006 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,027 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,048 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,067 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,086 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,106 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,124 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,142 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,159 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,177 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,194 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,212 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,229 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,247 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,264 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,283 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,303 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,322 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,341 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,361 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,380 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,399 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,412 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,424 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,435 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,445 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,445 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 02:28:03.207000832 of NaNs to the end of mission INFO 2025-06-26 19:28:17,454 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,454 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 02:28:03.207000832 of NaNs to the end of mission INFO 2025-06-26 19:28:17,463 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,463 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 02:28:03.207000832 of NaNs to the end of mission INFO 2025-06-26 19:28:17,472 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,472 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 02:28:03.207000832 of NaNs to the end of mission INFO 2025-06-26 19:28:17,481 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:17,481 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 02:28:03.207000832 of NaNs to the end of mission INFO 2025-06-26 19:28:17,636 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_1S.nc INFO 2025-06-26 19:28:21,010 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:28:30,987 create_products.py gulper_odv():522 [1] Wrote 7 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.075.06/dorado_2013.075.06_1S_Gulper.txt INFO 2025-06-26 19:28:30,987 process.py archive():337 [1] Archiving steps for 2013.075.06 INFO 2025-06-26 19:28:30,987 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06, BASE_PATH = /data/auv_data INFO 2025-06-26 19:28:30,988 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:28:30,989 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.075.06_1S.nc INFO 2025-06-26 19:28:31,002 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:28:31,003 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.075.06_cal.nc INFO 2025-06-26 19:28:31,045 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:28:31,046 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.075.06_align.nc INFO 2025-06-26 19:28:31,082 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:28:31,098 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,113 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,118 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,131 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,164 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,169 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,184 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,192 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013075/2013.075.06 done. INFO 2025-06-26 19:28:31,192 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:28:31,193 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.075.06_1S_Gulper.txt INFO 2025-06-26 19:28:31,198 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.075.06/dorado_2013.075.06_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:28:31,198 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.075.06/dorado_2013.075.06_processing.log /Volumes/AUVCTD/surveys/2013/netcdf