INFO 2025-06-26 18:59:17,644 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 18:59:17,644 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX missions - Initial engineering test from Yanwu & Frederic - ctdToUse = ctd1 INFO 2025-06-26 18:59:17,644 process.py process_mission():449 [1] Processing AUVCTD mission 2012.142.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 18:59:17,644 process.py download_process():165 [1] Download and processing steps for 2012.142.01 INFO 2025-06-26 18:59:17,644 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012142/2012.142.01 INFO 2025-06-26 18:59:17,645 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012142/2012.142.01 to /data/auv_data/dorado/missionlogs/2012.142.01 INFO 2025-06-26 18:59:21,077 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.142.01 INFO 2025-06-26 18:59:21,077 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/ctdDriver.log (6329382 bytes) INFO 2025-06-26 18:59:21,517 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/ctdDriver2.log (6329183 bytes) INFO 2025-06-26 18:59:21,986 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/gps.log (223268 bytes) INFO 2025-06-26 18:59:22,017 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/hydroscatlog.log (5543518 bytes) INFO 2025-06-26 18:59:22,601 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/navigation.log (22403958 bytes) INFO 2025-06-26 18:59:24,440 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/parosci.log (6712022 bytes) INFO 2025-06-26 18:59:25,093 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/tailCone.log (3962155 bytes) INFO 2025-06-26 18:59:25,697 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/biolume.log (4612866 bytes) INFO 2025-06-26 18:59:26,210 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 18:59:26,488 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.41 seconds INFO 2025-06-26 18:59:26,489 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2012.142.01/lopc.bin (67331000 bytes) INFO 2025-06-26 18:59:26,489 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 18:59:26 2025 INFO 2025-06-26 18:59:26,489 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2012.142.01/parosci.nc INFO 2025-06-26 18:59:26,490 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:59:26,490 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2012.142.01/parosci.nc INFO 2025-06-26 18:59:26,495 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1337617390.9, sensor_off_time = 1337633899.4 INFO 2025-06-26 18:59:26,495 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 16508 seconds. Expecting to read 33016 L frames from the lopc.bin file. INFO 2025-06-26 18:59:26,495 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 33016 records from the lopc.bin file. INFO 2025-06-26 18:59:26,707 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2012-05-21 16:23:10 Z and endTime = 2012-05-21 20:58:19 Z with 33016 records expected to be read from lopc.bin INFO 2025-06-26 18:59:26,707 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2012.142.01/lopc.bin INFO 2025-06-26 18:59:26,707 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2012.142.01/lopc.nc INFO 2025-06-26 18:59:26,708 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2012.142.01/lopc.nc INFO 2025-06-26 18:59:26,708 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2012.142.01 INFO 2025-06-26 18:59:26,709 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 18:59:26,713 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A01069135 WARNING 2025-06-26 18:59:26,713 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 18:59:26,928 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 18:59:26,928 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 18:59:26,928 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 18:59:27,123 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 18:59:27,125 process.py calibrate():227 [1] Calibration steps for 2012.142.01 INFO 2025-06-26 18:59:27,434 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 18:59:27,436 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 18:59:28,436 calibrate.py _nudge_pos():1806 [1] 130: 0.150 0.0007759 -0.0074104 11955 39.85 2.886 -34.461 2012-05-21T17:05:10.022168832 INFO 2025-06-26 18:59:30,723 calibrate.py _nudge_pos():1806 [1] 363: 0.150 0.0002497 -0.0016460 2170 7.23 5.119 -42.185 2012-05-21T17:16:16.016545280 INFO 2025-06-26 18:59:31,500 calibrate.py _nudge_pos():1806 [1] 444: 0.150 0.0002426 -0.0073703 9500 31.66 1.136 -43.133 2012-05-21T17:49:16.020905472 INFO 2025-06-26 18:59:31,569 calibrate.py _nudge_pos():1806 [1] 451: 0.160 -0.0000217 0.0000166 45 0.15 -21.945 20.917 2012-05-21T17:49:31.019878144 INFO 2025-06-26 18:59:32,919 calibrate.py _nudge_pos():1806 [1] 581: 0.170 0.0002052 -0.0000737 4170 13.90 2.189 -0.983 2012-05-21T18:05:34.013908480 INFO 2025-06-26 18:59:39,948 calibrate.py _nudge_pos():1806 [1] 1280: 0.160 0.0017034 -0.0067887 10580 35.26 7.160 -35.673 2012-05-21T18:52:28.021135872 INFO 2025-06-26 18:59:41,475 calibrate.py _nudge_pos():1806 [1] 1423: 0.160 0.0016321 -0.0061421 8800 29.33 8.248 -38.805 2012-05-21T19:24:10.020839936 INFO 2025-06-26 18:59:48,344 calibrate.py _nudge_pos():1806 [1] 2105: 0.160 -0.0001622 -0.0066051 11205 37.35 -0.644 -32.772 2012-05-21T20:12:52.020669184 INFO 2025-06-26 18:59:50,365 calibrate.py _nudge_pos():1806 [1] 2308: 0.180 -0.0000141 0.0000067 50 0.16 -12.766 7.554 2012-05-21T20:16:24.016146432 INFO 2025-06-26 18:59:50,981 calibrate.py _nudge_pos():1806 [1] 2370: 0.170 0.0013665 -0.0062628 8655 28.85 7.021 -40.230 2012-05-21T20:46:16.013386240 INFO 2025-06-26 18:59:51,076 calibrate.py _nudge_pos():1806 [1] 2379: 0.180 -0.0000518 0.0000884 30 0.10 -79.413 169.387 2012-05-21T20:46:30.012427264 INFO 2025-06-26 18:59:58,024 calibrate.py _nudge_pos():1862 [1] 3052: - - - 2 0.00 - - INFO 2025-06-26 18:59:58,024 calibrate.py _nudge_pos():1868 [1] Points in final series = 82358 WARNING 2025-06-26 18:59:58,133 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 18:59:58,247 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 65982 INFO 2025-06-26 18:59:58,765 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:59:59,384 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:59:59,871 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:59:59,873 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.142.01/ctd1.nc INFO 2025-06-26 18:59:59,875 calibrate.py _range_qc_combined_nc():898 [1] Setting 14 ctd1_salinity values to NaN INFO 2025-06-26 18:59:59,875 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 18:59:59,875 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:00:00,494 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:00,986 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:00,988 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.142.01/ctd2.nc INFO 2025-06-26 19:00:00,990 calibrate.py _range_qc_combined_nc():898 [1] Setting 7 ctd2_salinity values to NaN INFO 2025-06-26 19:00:00,990 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 19:00:00,990 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:00:00,990 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.142.01 INFO 2025-06-26 19:00:01,005 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:00:01,806 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [365280 365281 365282] INFO 2025-06-26 19:00:01,953 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:00:17,371 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2012.142.01 ERROR 2025-06-26 19:00:17,372 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.142.01 INFO 2025-06-26 19:00:17,438 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_cal.nc INFO 2025-06-26 19:00:17,560 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 19:00:17,569 process.py align():251 [1] Alignment steps for 2012.142.01 INFO 2025-06-26 19:00:17,613 align.py process_cal():139 [1] Processing dorado_2012.142.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.142.01 INFO 2025-06-26 19:00:17,645 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:17,655 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:17,723 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:17,729 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:17,797 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:17,802 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:17,843 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:00:17,843 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:00:17,868 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:17,874 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:17,939 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:17,944 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,000 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,005 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,064 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,069 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,127 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,132 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,191 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,196 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,256 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,261 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,321 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,326 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,385 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,390 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,451 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,455 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,516 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,521 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,580 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,585 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,643 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,649 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,714 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,719 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,777 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,782 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,848 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,854 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,910 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,915 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:18,974 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:18,979 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:19,038 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:19,044 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:19,104 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:19,110 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:19,165 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:19,170 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:19,227 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:19,232 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:19,286 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.142.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:19,291 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:19,368 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:00:19,424 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:00:19,511 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:00:19,984 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:20,031 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_align.nc INFO 2025-06-26 19:00:20,208 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 19:00:20,212 process.py resample():273 [1] Resampling steps for 2012.142.01 INFO 2025-06-26 19:00:20,212 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:00:20,251 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_align.nc mission netCDF file INFO 2025-06-26 19:00:20,256 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_align.nc mission netCDF file INFO 2025-06-26 19:00:20,258 resample.py get_mission_start_end():1145 [1] navigation: 2012-05-21T16:23:47.872207872 to 2012-05-21T20:58:19.413830144 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 19:00:20,259 resample.py get_mission_start_end():1145 [1] hs2 : 2012-05-21T16:23:16.814335232 to 2012-05-21T20:58:19.283838720 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 19:00:20,261 resample.py get_mission_start_end():1145 [1] ctd1 : 2012-05-21T16:23:38.972817408 to 2012-05-21T20:58:19.343834624 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:00:20,263 resample.py get_mission_start_end():1145 [1] ctd2 : 2012-05-21T16:23:39.202801664 to 2012-05-21T20:58:19.313836800 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 19:00:20,264 resample.py get_mission_start_end():1145 [1] biolume : 2012-05-21T16:23:09.984769024 to 2012-05-21T20:58:18.063888128 (0 days 00:00:01.389938944 before mission_end) INFO 2025-06-26 19:00:20,266 resample.py get_mission_start_end():1145 [1] tailcone : 2012-05-21T16:23:12.654620416 to 2012-05-21T20:58:19.453827072 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:00:20,266 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_align.nc mission netCDF file INFO 2025-06-26 19:00:20,267 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,477 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,517 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,555 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,593 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,627 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,661 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,693 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,726 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,756 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,787 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,818 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,848 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,878 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,910 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,941 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:20,972 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,002 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,038 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,072 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,106 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,137 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,168 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,200 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,232 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,249 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,264 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:21,270 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:00:21,270 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:00:21,886 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:00:22,038 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:00:22,102 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:00:22,133 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:00:22,156 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:00:22,157 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:00:22,197 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:22,418 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_1S.nc INFO 2025-06-26 19:00:25,019 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:00:26,126 create_products.py gulper_odv():522 [1] Wrote 1 Gulper data lines to /data/auv_data/dorado/missionodvs/2012.142.01/dorado_2012.142.01_1S_Gulper.txt INFO 2025-06-26 19:00:26,127 process.py archive():337 [1] Archiving steps for 2012.142.01 INFO 2025-06-26 19:00:26,127 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:00:26,128 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01 files to /Volumes/AUVCTD/surveys/2012/netcdf INFO 2025-06-26 19:00:26,130 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.142.01_1S.nc INFO 2025-06-26 19:00:26,151 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:26,153 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.142.01_cal.nc INFO 2025-06-26 19:00:26,289 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:26,290 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.142.01_align.nc INFO 2025-06-26 19:00:26,493 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:26,524 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,555 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,563 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,587 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,668 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,703 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,740 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,797 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,806 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012142/2012.142.01 done. INFO 2025-06-26 19:00:26,806 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:00:26,809 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2012/odv/dorado_2012.142.01_1S_Gulper.txt INFO 2025-06-26 19:00:26,818 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2012.142.01/dorado_2012.142.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2012/odv done. INFO 2025-06-26 19:00:26,818 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.142.01/dorado_2012.142.01_processing.log /Volumes/AUVCTD/surveys/2012/netcdf