INFO 2025-06-26 19:57:14,743 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 19:57:14,743 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Autonomy group's short missions in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 19:57:14,743 process.py process_mission():449 [1] Processing AUVCTD mission 2013.282.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:57:14,743 process.py download_process():165 [1] Download and processing steps for 2013.282.00 INFO 2025-06-26 19:57:14,743 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013282/2013.282.00 INFO 2025-06-26 19:57:14,743 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013282/2013.282.00 to /data/auv_data/dorado/missionlogs/2013.282.00 INFO 2025-06-26 19:57:17,952 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.282.00 INFO 2025-06-26 19:57:17,952 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/ctdDriver.log (5333766 bytes) INFO 2025-06-26 19:57:18,351 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/ctdDriver2.log (5342879 bytes) INFO 2025-06-26 19:57:18,737 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/gps.log (301532 bytes) INFO 2025-06-26 19:57:18,776 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/hydroscatlog.log (4680502 bytes) INFO 2025-06-26 19:57:19,253 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/navigation.log (18910118 bytes) INFO 2025-06-26 19:57:20,606 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/parosci.log (6581750 bytes) INFO 2025-06-26 19:57:21,168 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/tailCone.log (3345883 bytes) INFO 2025-06-26 19:57:21,579 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/biolume.log (3895482 bytes) INFO 2025-06-26 19:57:21,962 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:57:22,161 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.21 seconds INFO 2025-06-26 19:57:22,161 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.282.00/lopc.bin (32160167 bytes) INFO 2025-06-26 19:57:22,161 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:57:22 2025 INFO 2025-06-26 19:57:22,161 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.282.00/parosci.nc INFO 2025-06-26 19:57:22,162 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:57:22,162 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.282.00/parosci.nc INFO 2025-06-26 19:57:22,165 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1381332863.7, sensor_off_time = 1381346802.2 INFO 2025-06-26 19:57:22,165 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 13938 seconds. Expecting to read 27876 L frames from the lopc.bin file. INFO 2025-06-26 19:57:22,165 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 27876 records from the lopc.bin file. INFO 2025-06-26 19:57:22,330 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-09 15:34:23 Z and endTime = 2013-10-09 19:26:42 Z with 27876 records expected to be read from lopc.bin INFO 2025-06-26 19:57:22,330 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.282.00/lopc.bin INFO 2025-06-26 19:57:22,330 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.282.00/lopc.nc INFO 2025-06-26 19:57:22,330 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.282.00/lopc.nc INFO 2025-06-26 19:57:22,331 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.282.00 INFO 2025-06-26 19:57:22,331 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:57:22,423 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:57:22,423 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:57:22,423 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:57:26,846 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:57:26,846 process.py calibrate():227 [1] Calibration steps for 2013.282.00 INFO 2025-06-26 19:57:26,993 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 19:57:26,995 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:57:27,786 calibrate.py _nudge_pos():1806 [1] 115: 0.200 -0.0002189 -0.0003782 3057 10.19 -3.183 -6.875 2013-10-09T15:46:27.977120512 INFO 2025-06-26 19:57:29,874 calibrate.py _nudge_pos():1806 [1] 340: 0.010 0.0008556 0.0002269 5360 17.86 7.097 2.354 2013-10-09T16:08:04.178324480 INFO 2025-06-26 19:57:31,965 calibrate.py _nudge_pos():1806 [1] 567: 0.200 -0.0006368 -0.0003673 5859 19.53 -4.833 -3.486 2013-10-09T16:31:21.982568448 INFO 2025-06-26 19:57:33,557 calibrate.py _nudge_pos():1806 [1] 740: 0.010 -0.0000127 0.0000141 20 0.06 -29.603 41.174 2013-10-09T16:34:18.180498176 INFO 2025-06-26 19:57:33,687 calibrate.py _nudge_pos():1806 [1] 754: 0.010 0.0002313 -0.0005892 2055 6.85 5.006 -15.947 2013-10-09T16:41:22.181452032 INFO 2025-06-26 19:57:42,359 calibrate.py _nudge_pos():1806 [1] 1690: 0.010 -0.0008788 -0.0005176 5495 18.31 -7.110 -5.237 2013-10-09T17:15:16.182113536 INFO 2025-06-26 19:57:44,175 calibrate.py _nudge_pos():1806 [1] 1885: 0.020 0.0012983 0.0000551 5030 16.76 11.476 0.609 2013-10-09T17:35:16.179907840 INFO 2025-06-26 19:57:46,267 calibrate.py _nudge_pos():1806 [1] 2109: 0.010 -0.0010808 -0.0008820 3145 10.48 -15.282 -15.595 2013-10-09T17:49:28.181541632 INFO 2025-06-26 19:57:47,393 calibrate.py _nudge_pos():1806 [1] 2229: 0.020 0.0000587 -0.0003733 1505 5.01 1.736 -13.796 2013-10-09T17:56:28.182769664 INFO 2025-06-26 19:57:55,324 calibrate.py _nudge_pos():1806 [1] 3076: 0.020 -0.0006421 -0.0005478 3450 11.50 -8.275 -8.830 2013-10-09T18:22:04.177547008 INFO 2025-06-26 19:57:57,010 calibrate.py _nudge_pos():1806 [1] 3255: 0.030 0.0008966 0.0002945 5560 18.53 7.169 2.945 2013-10-09T18:43:34.179175680 INFO 2025-06-26 19:57:57,652 calibrate.py _nudge_pos():1806 [1] 3323: 0.020 0.0000159 -0.0000091 20 0.06 37.069 -26.431 2013-10-09T18:44:45.184311552 INFO 2025-06-26 19:57:59,057 calibrate.py _nudge_pos():1806 [1] 3472: 0.020 -0.0000284 -0.0000573 20 0.06 -66.379 -167.642 2013-10-09T18:47:17.183898880 INFO 2025-06-26 19:57:59,086 calibrate.py _nudge_pos():1806 [1] 3475: 0.030 -0.0009730 -0.0004094 5785 19.28 -7.478 -3.935 2013-10-09T19:06:36.174502656 INFO 2025-06-26 19:58:00,256 calibrate.py _nudge_pos():1806 [1] 3598: 0.040 -0.0003311 -0.0000731 820 2.73 -17.970 -4.961 2013-10-09T19:11:22.174909952 INFO 2025-06-26 19:58:05,306 calibrate.py _nudge_pos():1806 [1] 4131: 0.040 0.0003724 -0.0005243 1720 5.73 9.630 -16.955 2013-10-09T19:25:58.174899968 INFO 2025-06-26 19:58:05,723 calibrate.py _nudge_pos():1862 [1] 4139: - - - 0 0.00 - - INFO 2025-06-26 19:58:05,723 calibrate.py _nudge_pos():1868 [1] Points in final series = 69423 INFO 2025-06-26 19:58:06,340 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:58:06,862 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 50 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:58:07,271 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 50 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:58:07,273 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.282.00/ctd1.nc INFO 2025-06-26 19:58:07,274 calibrate.py _range_qc_combined_nc():898 [1] Setting 102 ctd1_salinity values to NaN INFO 2025-06-26 19:58:07,275 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 19:58:07,275 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:58:07,764 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:58:08,194 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:58:08,196 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.282.00/ctd2.nc INFO 2025-06-26 19:58:08,197 calibrate.py _range_qc_combined_nc():898 [1] Setting 68 ctd2_salinity values to NaN INFO 2025-06-26 19:58:08,198 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 19:58:08,198 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:58:08,198 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.282.00 INFO 2025-06-26 19:58:08,209 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:58:08,869 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86] INFO 2025-06-26 19:58:08,991 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:58:21,544 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.282.00 ERROR 2025-06-26 19:58:21,544 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.282.00 INFO 2025-06-26 19:58:21,600 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_cal.nc INFO 2025-06-26 19:58:21,714 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, 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 19:58:21,720 process.py align():251 [1] Alignment steps for 2013.282.00 INFO 2025-06-26 19:58:21,756 align.py process_cal():139 [1] Processing dorado_2013.282.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.282.00 INFO 2025-06-26 19:58:21,779 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:58:21,783 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:58:21,833 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:58:21,837 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:58:21,887 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:58:21,891 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:58:21,920 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:58:21,921 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:58:21,939 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:58:21,944 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:58:21,992 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:21,996 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,043 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,048 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,093 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,097 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,141 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,144 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,189 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,192 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,235 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,239 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,283 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,287 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,332 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,335 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,380 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,383 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,427 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,430 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,476 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,480 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,523 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,527 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,572 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,576 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,620 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,623 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,669 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,673 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,719 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,724 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,771 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,775 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,819 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,823 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,868 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,872 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,916 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,921 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:22,966 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:22,970 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:23,014 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.282.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:58:23,018 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:58:23,085 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:58:23,127 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:58:23,196 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:58:23,559 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:58:23,595 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_align.nc INFO 2025-06-26 19:58:23,709 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, 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 19:58:23,711 process.py resample():273 [1] Resampling steps for 2013.282.00 INFO 2025-06-26 19:58:23,712 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:58:23,744 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_align.nc mission netCDF file INFO 2025-06-26 19:58:23,749 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_align.nc mission netCDF file INFO 2025-06-26 19:58:23,750 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-09T15:34:59.194305280 to 2013-10-09T19:26:42.181885440 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 19:58:23,752 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-09T15:34:28.996374016 to 2013-10-09T19:26:42.141888256 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 19:58:23,754 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-09T15:35:14.383264768 to 2013-10-09T19:26:42.081892352 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 19:58:23,756 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-09T15:34:49.834946304 to 2013-10-09T19:26:42.271879168 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:58:23,757 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-09T15:34:22.716770048 to 2013-10-09T19:26:41.291912192 (0 days 00:00:00.979966976 before mission_end) INFO 2025-06-26 19:58:23,758 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-09T15:34:23.166773248 to 2013-10-09T19:26:42.241881344 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 19:58:23,759 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_align.nc mission netCDF file INFO 2025-06-26 19:58:23,760 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:23,920 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:23,949 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:23,977 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,006 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,033 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,058 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,084 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,110 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,134 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,158 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,180 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,202 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,224 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,246 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,268 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,290 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,312 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,337 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,362 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,388 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,412 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,436 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,461 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,487 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,501 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,513 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:24,519 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:58:24,519 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:58:25,048 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:58:25,150 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:58:25,202 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:58:25,224 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:58:25,244 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:58:25,244 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:58:25,276 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:58:25,458 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_1S.nc INFO 2025-06-26 19:58:26,514 create_products.py gulper_odv():401 [1] No gulper times found for 2013.282.00 INFO 2025-06-26 19:58:26,514 process.py archive():337 [1] Archiving steps for 2013.282.00 INFO 2025-06-26 19:58:26,514 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:58:26,516 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:58:26,517 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.282.00_1S.nc INFO 2025-06-26 19:58:26,537 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:58:26,538 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.282.00_cal.nc INFO 2025-06-26 19:58:26,632 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:58:26,634 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.282.00_align.nc INFO 2025-06-26 19:58:26,769 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:58:26,789 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,807 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,813 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,830 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,883 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,905 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,921 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,961 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,973 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013282/2013.282.00 done. INFO 2025-06-26 19:58:26,973 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:58:26,973 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.282.00/dorado_2013.282.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf