INFO 2025-06-26 19:55:29,890 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 19:55:29,890 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:55:29,890 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.280.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:55:29,890 process.py download_process():165 [1] Download and processing steps for 2013.280.01 INFO 2025-06-26 19:55:29,891 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013280/2013.280.01 INFO 2025-06-26 19:55:29,891 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013280/2013.280.01 to /data/auv_data/dorado/missionlogs/2013.280.01 INFO 2025-06-26 19:55:32,874 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.280.01 INFO 2025-06-26 19:55:32,874 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/ctdDriver.log (5614374 bytes) INFO 2025-06-26 19:55:33,271 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/ctdDriver2.log (5614463 bytes) INFO 2025-06-26 19:55:33,690 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/gps.log (502340 bytes) INFO 2025-06-26 19:55:33,750 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/hydroscatlog.log (4915114 bytes) INFO 2025-06-26 19:55:34,247 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.280.01/hydroscatlog.log: [1] INFO 2025-06-26 19:55:34,261 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/navigation.log (19858310 bytes) INFO 2025-06-26 19:55:35,664 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/parosci.log (6912038 bytes) INFO 2025-06-26 19:55:36,246 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/tailCone.log (3513211 bytes) INFO 2025-06-26 19:55:36,679 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/biolume.log (4090590 bytes) INFO 2025-06-26 19:55:37,085 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:55:37,294 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.42 seconds INFO 2025-06-26 19:55:37,294 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.280.01/lopc.bin (32272873 bytes) INFO 2025-06-26 19:55:37,295 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:55:37 2025 INFO 2025-06-26 19:55:37,295 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.280.01/parosci.nc INFO 2025-06-26 19:55:37,295 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:55:37,295 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.280.01/parosci.nc INFO 2025-06-26 19:55:37,298 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1381158993.0, sensor_off_time = 1381173629.7 INFO 2025-06-26 19:55:37,298 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 14636 seconds. Expecting to read 29272 L frames from the lopc.bin file. INFO 2025-06-26 19:55:37,298 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 29272 records from the lopc.bin file. INFO 2025-06-26 19:55:37,470 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-07 15:16:33 Z and endTime = 2013-10-07 19:20:29 Z with 29272 records expected to be read from lopc.bin INFO 2025-06-26 19:55:37,470 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.280.01/lopc.bin INFO 2025-06-26 19:55:37,470 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.280.01/lopc.nc INFO 2025-06-26 19:55:37,470 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.280.01/lopc.nc INFO 2025-06-26 19:55:37,471 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.280.01 INFO 2025-06-26 19:55:37,471 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:55:37,505 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:55:37,505 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:55:37,505 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:55:39,952 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:55:39,953 process.py calibrate():227 [1] Calibration steps for 2013.280.01 INFO 2025-06-26 19:55:40,112 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 19:55:40,114 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:55:40,846 calibrate.py _nudge_pos():1806 [1] 109: 0.160 -0.0006690 -0.0006154 5800 19.33 -5.128 -5.899 2013-10-07T15:37:39.186636288 INFO 2025-06-26 19:55:42,903 calibrate.py _nudge_pos():1806 [1] 330: 0.160 0.0013908 -0.0000036 3160 10.53 19.569 -0.063 2013-10-07T15:51:51.188270080 INFO 2025-06-26 19:55:43,990 calibrate.py _nudge_pos():1806 [1] 445: 0.170 0.0008426 -0.0001235 3600 12.00 10.408 -1.908 2013-10-07T16:05:45.181137664 INFO 2025-06-26 19:55:46,086 calibrate.py _nudge_pos():1806 [1] 669: 0.160 -0.0016680 -0.0009964 3535 11.78 -20.982 -15.674 2013-10-07T16:21:15.187427840 INFO 2025-06-26 19:55:47,348 calibrate.py _nudge_pos():1806 [1] 804: 0.160 -0.0000903 -0.0000279 1010 3.36 -3.980 -1.539 2013-10-07T16:26:51.184410368 INFO 2025-06-26 19:55:51,914 calibrate.py _nudge_pos():1806 [1] 1294: 0.170 0.0004843 -0.0006779 2115 7.05 10.184 -17.825 2013-10-07T16:42:03.181934336 INFO 2025-06-26 19:56:23,594 calibrate.py _nudge_pos():1806 [1] 4681: 0.170 -0.0008613 -0.0009799 4130 13.76 -9.273 -13.193 2013-10-07T17:52:15.183392512 INFO 2025-06-26 19:56:25,705 calibrate.py _nudge_pos():1806 [1] 4905: 0.180 -0.0004659 -0.0000472 3685 12.28 -5.621 -0.712 2013-10-07T18:08:15.187627520 INFO 2025-06-26 19:56:27,394 calibrate.py _nudge_pos():1806 [1] 5084: 0.170 0.0020948 -0.0001036 6310 21.03 14.761 -0.913 2013-10-07T18:32:15.188980736 INFO 2025-06-26 19:56:29,633 calibrate.py _nudge_pos():1806 [1] 5319: 0.180 -0.0014736 -0.0009322 2910 9.70 -22.520 -17.814 2013-10-07T18:45:51.183081472 INFO 2025-06-26 19:56:30,763 calibrate.py _nudge_pos():1806 [1] 5438: 0.180 0.0000157 -0.0005732 2170 7.23 0.321 -14.690 2013-10-07T18:55:03.185266688 INFO 2025-06-26 19:56:45,349 calibrate.py _nudge_pos():1862 [1] 6927: - - - 2 0.00 - - INFO 2025-06-26 19:56:45,349 calibrate.py _nudge_pos():1868 [1] Points in final series = 72999 INFO 2025-06-26 19:56:53,170 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:56:53,721 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:56:54,152 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:56:54,154 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.280.01/ctd1.nc INFO 2025-06-26 19:56:54,155 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:56:54,156 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 19:56:54,156 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:56:54,674 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:56:55,105 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:56:55,107 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.280.01/ctd2.nc INFO 2025-06-26 19:56:55,108 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:56:55,109 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 19:56:55,109 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:56:55,109 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.280.01 INFO 2025-06-26 19:56:55,121 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:56:55,813 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67] INFO 2025-06-26 19:56:55,939 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:57:09,128 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.280.01 ERROR 2025-06-26 19:57:09,128 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.280.01 INFO 2025-06-26 19:57:09,187 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_cal.nc INFO 2025-06-26 19:57:09,298 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 19:57:09,304 process.py align():251 [1] Alignment steps for 2013.280.01 INFO 2025-06-26 19:57:09,337 align.py process_cal():139 [1] Processing dorado_2013.280.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.280.01 INFO 2025-06-26 19:57:09,360 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:57:09,364 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:57:09,418 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:57:09,422 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:57:09,472 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:57:09,476 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:57:09,506 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:57:09,506 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:57:09,526 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:57:09,529 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:57:09,579 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,583 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,627 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,631 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,675 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,679 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,722 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,726 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,771 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,775 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,819 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,822 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,867 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,871 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,915 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,918 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:09,963 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:09,966 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,011 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,016 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,062 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,066 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,111 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,114 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,161 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,165 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,210 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,213 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,258 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,262 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,308 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,312 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,358 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,362 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,407 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,411 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,458 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,461 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,507 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,511 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,558 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,562 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,607 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:57:10,611 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:57:10,669 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:57:10,713 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:57:10,786 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:57:11,171 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:57:11,208 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_align.nc INFO 2025-06-26 19:57:11,323 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 19:57:11,326 process.py resample():273 [1] Resampling steps for 2013.280.01 INFO 2025-06-26 19:57:11,326 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:57:11,357 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_align.nc mission netCDF file INFO 2025-06-26 19:57:11,362 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_align.nc mission netCDF file INFO 2025-06-26 19:57:11,364 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-07T15:17:09.800855040 to 2013-10-07T19:20:29.590700544 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 19:57:11,365 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-07T15:16:37.593061120 to 2013-10-07T19:20:29.530704640 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 19:57:11,367 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-07T15:16:50.962145280 to 2013-10-07T19:20:29.640697344 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:57:11,369 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-07T15:16:50.972144640 to 2013-10-07T19:20:29.640697344 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:57:11,370 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-07T15:16:31.193465344 to 2013-10-07T19:20:29.010706176 (0 days 00:00:00.629991168 before mission_end) INFO 2025-06-26 19:57:11,372 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-07T15:16:33.573336576 to 2013-10-07T19:20:29.610699520 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 19:57:11,372 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_align.nc mission netCDF file INFO 2025-06-26 19:57:11,373 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,542 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,573 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,602 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,631 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,657 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,683 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,708 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,732 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,755 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,778 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,802 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,825 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,847 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,870 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,893 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,916 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,939 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,965 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:11,989 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,014 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,038 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,063 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,087 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,111 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,123 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,135 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:12,139 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:57:12,139 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:57:12,695 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:57:12,797 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:57:12,849 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:57:12,872 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:57:12,891 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:57:12,891 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:57:12,924 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:57:13,110 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_1S.nc INFO 2025-06-26 19:57:14,231 create_products.py gulper_odv():401 [1] No gulper times found for 2013.280.01 INFO 2025-06-26 19:57:14,231 process.py archive():337 [1] Archiving steps for 2013.280.01 INFO 2025-06-26 19:57:14,231 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:57:14,233 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:57:14,234 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.280.01_1S.nc INFO 2025-06-26 19:57:14,252 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:57:14,253 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.280.01_cal.nc INFO 2025-06-26 19:57:14,354 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:57:14,356 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.280.01_align.nc INFO 2025-06-26 19:57:14,496 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:57:14,518 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,537 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,544 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,562 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,614 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,637 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,655 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,696 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,706 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013280/2013.280.01 done. INFO 2025-06-26 19:57:14,706 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:57:14,707 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.280.01/dorado_2013.280.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf