INFO 2025-06-26 20:24:11,759 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 20:24:11,759 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Summer 2014 in Bodega Bay - ctdToUse = ctd2 INFO 2025-06-26 20:24:11,759 process.py process_mission():449 [1] Processing SIMZ July 2014 mission 2014.210.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:24:11,759 process.py download_process():165 [1] Download and processing steps for 2014.210.02 INFO 2025-06-26 20:24:11,760 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014210/2014.210.02 INFO 2025-06-26 20:24:11,760 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014210/2014.210.02 to /data/auv_data/dorado/missionlogs/2014.210.02 INFO 2025-06-26 20:24:15,282 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.210.02 INFO 2025-06-26 20:24:15,283 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/ctdDriver.log (3683334 bytes) INFO 2025-06-26 20:24:15,541 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/ctdDriver2.log (3683231 bytes) INFO 2025-06-26 20:24:15,808 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/gps.log (38948 bytes) INFO 2025-06-26 20:24:15,820 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/hydroscatlog.log (3228898 bytes) INFO 2025-06-26 20:24:16,141 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.210.02/hydroscatlog.log: [38274] INFO 2025-06-26 20:24:16,148 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/navigation.log (13786146 bytes) INFO 2025-06-26 20:24:17,140 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/isuslog.log (237781 bytes) INFO 2025-06-26 20:24:17,167 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/parosci.log (4533062 bytes) INFO 2025-06-26 20:24:17,526 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.210.02/parosci.log: [1 2 3 4 5] INFO 2025-06-26 20:24:17,536 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/tailCone.log (2308699 bytes) INFO 2025-06-26 20:24:17,820 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/biolume.log (2688766 bytes) INFO 2025-06-26 20:24:18,086 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:24:18,219 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.94 seconds INFO 2025-06-26 20:24:18,219 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.210.02/lopc.bin (31207997 bytes) INFO 2025-06-26 20:24:18,220 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:24:18 2025 INFO 2025-06-26 20:24:18,220 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.210.02/parosci.nc INFO 2025-06-26 20:24:18,220 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:24:18,220 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.210.02/parosci.nc INFO 2025-06-26 20:24:18,223 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1406656013.8, sensor_off_time = 1406665629.6 INFO 2025-06-26 20:24:18,223 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 9615 seconds. Expecting to read 19230 L frames from the lopc.bin file. INFO 2025-06-26 20:24:18,223 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 19230 records from the lopc.bin file. INFO 2025-06-26 20:24:18,335 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-07-29 17:46:53 Z and endTime = 2014-07-29 20:27:09 Z with 19230 records expected to be read from lopc.bin INFO 2025-06-26 20:24:18,335 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.210.02/lopc.bin INFO 2025-06-26 20:24:18,335 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.210.02/lopc.nc INFO 2025-06-26 20:24:18,335 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.210.02/lopc.nc INFO 2025-06-26 20:24:18,336 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.210.02 INFO 2025-06-26 20:24:18,336 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:24:18,339 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:24:18,393 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:24:18,394 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:24:18,394 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:24:28,660 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:24:28,661 process.py calibrate():227 [1] Calibration steps for 2014.210.02 INFO 2025-06-26 20:24:28,854 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 20:24:28,856 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:24:29,601 calibrate.py _nudge_pos():1806 [1] 118: 0.150 -0.0002195 -0.0000235 1164 3.88 -8.224 -1.123 2014-07-29T17:52:40.138325248 INFO 2025-06-26 20:24:30,214 calibrate.py _nudge_pos():1806 [1] 184: 0.160 -0.0003325 0.0000513 2645 8.81 -5.484 1.080 2014-07-29T18:02:34.137633536 INFO 2025-06-26 20:24:30,815 calibrate.py _nudge_pos():1806 [1] 249: 0.160 0.0028960 0.0045489 12130 40.43 10.413 20.849 2014-07-29T18:44:04.137056768 INFO 2025-06-26 20:24:31,462 calibrate.py _nudge_pos():1806 [1] 319: 0.180 -0.0017669 0.0011144 13245 44.15 -5.820 4.677 2014-07-29T19:29:22.130861568 INFO 2025-06-26 20:24:32,140 calibrate.py _nudge_pos():1806 [1] 391: 0.180 -0.0049623 0.0017729 9815 32.71 -22.059 10.042 2014-07-29T20:03:16.131522816 INFO 2025-06-26 20:24:32,770 calibrate.py _nudge_pos():1806 [1] 458: 0.180 -0.0023273 0.0005310 3900 13.00 -26.039 7.570 2014-07-29T20:17:22.133567744 INFO 2025-06-26 20:24:33,382 calibrate.py _nudge_pos():1806 [1] 523: 0.180 -0.0003796 0.0001629 2590 8.63 -6.397 3.498 2014-07-29T20:27:04.133698304 INFO 2025-06-26 20:24:33,436 calibrate.py _nudge_pos():1862 [1] 482: - - - 2 0.00 - - INFO 2025-06-26 20:24:33,436 calibrate.py _nudge_pos():1868 [1] Points in final series = 47860 INFO 2025-06-26 20:24:40,051 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:24:40,429 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:24:40,721 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:24:40,723 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.210.02/ctd1.nc INFO 2025-06-26 20:24:40,724 calibrate.py _range_qc_combined_nc():898 [1] Setting 179 ctd1_salinity values to NaN INFO 2025-06-26 20:24:40,724 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 20:24:40,725 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:24:41,076 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:24:41,372 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:24:41,374 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.210.02/ctd2.nc INFO 2025-06-26 20:24:41,375 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:24:41,375 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 20:24:41,375 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:24:41,395 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:24:41,854 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] INFO 2025-06-26 20:24:41,939 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:24:50,637 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.210.02 ERROR 2025-06-26 20:24:50,637 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.210.02 INFO 2025-06-26 20:24:50,677 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_cal.nc INFO 2025-06-26 20:24:50,769 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, isus_nitrate, isus_quality, isus_temp, isus_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 20:24:50,775 process.py align():251 [1] Alignment steps for 2014.210.02 INFO 2025-06-26 20:24:50,807 align.py process_cal():139 [1] Processing dorado_2014.210.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.210.02 INFO 2025-06-26 20:24:50,824 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:24:50,827 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:24:50,864 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:24:50,868 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:24:50,906 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:24:50,909 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:24:50,931 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:24:50,931 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:24:50,945 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:24:50,949 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:24:50,986 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:50,989 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,022 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,025 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,059 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,062 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,095 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,099 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,132 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,136 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,168 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,172 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,206 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,209 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,242 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,245 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,281 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,284 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,317 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,320 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,354 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,357 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,390 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,393 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,426 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,430 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,463 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,466 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,501 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,504 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,537 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,540 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,574 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,577 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,610 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,613 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,650 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,654 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,687 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,690 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,725 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,729 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,762 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.210.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:24:51,765 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:24:51,807 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:24:51,838 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:24:51,869 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:24:51,902 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:24:51,936 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:24:51,987 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:24:52,249 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:24:52,278 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_align.nc INFO 2025-06-26 20:24:52,371 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, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_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 20:24:52,373 process.py resample():273 [1] Resampling steps for 2014.210.02 INFO 2025-06-26 20:24:52,374 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:24:52,403 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_align.nc mission netCDF file INFO 2025-06-26 20:24:52,408 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_align.nc mission netCDF file INFO 2025-06-26 20:24:52,409 resample.py get_mission_start_end():1145 [1] navigation: 2014-07-29T17:47:37.549054208 to 2014-07-29T20:27:09.533328384 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 20:24:52,411 resample.py get_mission_start_end():1145 [1] hs2 : 2014-07-29T17:46:58.791709184 to 2014-07-29T20:27:09.543327488 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 20:24:52,412 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-07-29T17:47:19.570285824 to 2014-07-29T20:27:09.573325312 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:24:52,413 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-07-29T17:47:19.880264448 to 2014-07-29T20:27:09.403337216 (0 days 00:00:00.169988096 before mission_end) INFO 2025-06-26 20:24:52,415 resample.py get_mission_start_end():1145 [1] isus : 2014-07-29T17:48:07.147026432 to 2014-07-29T20:27:09.073359616 (0 days 00:00:00.499965696 before mission_end) INFO 2025-06-26 20:24:52,416 resample.py get_mission_start_end():1145 [1] biolume : 2014-07-29T17:46:51.292188672 to 2014-07-29T20:27:08.353374720 (0 days 00:00:01.219950592 before mission_end) INFO 2025-06-26 20:24:52,417 resample.py get_mission_start_end():1145 [1] tailcone : 2014-07-29T17:46:52.312153088 to 2014-07-29T20:27:09.573325312 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:24:52,418 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_align.nc mission netCDF file INFO 2025-06-26 20:24:52,418 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,536 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,558 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,579 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,600 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,620 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,639 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,658 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,676 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,694 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,713 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,732 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,751 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,768 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,786 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,803 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,820 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,838 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,857 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,877 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,896 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,914 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,933 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,951 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,970 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,982 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:52,993 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:53,003 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:53,013 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:53,022 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:53,026 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:24:53,026 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:24:53,389 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:24:53,446 resample.py add_biolume_proxies():633 [1] Zero flow values found: 9618 of 9618 - replaced with 350 ml/s INFO 2025-06-26 20:24:53,447 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:24:53,482 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:24:53,498 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:24:53,512 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:24:53,512 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:24:53,538 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:24:53,702 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_1S.nc INFO 2025-06-26 20:24:55,415 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 20:25:07,739 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.210.02/dorado_2014.210.02_1S_Gulper.txt INFO 2025-06-26 20:25:07,739 process.py archive():337 [1] Archiving steps for 2014.210.02 INFO 2025-06-26 20:25:07,739 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02, BASE_PATH = /data/auv_data INFO 2025-06-26 20:25:07,740 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:25:07,741 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.210.02_1S.nc INFO 2025-06-26 20:25:07,756 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:25:07,757 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.210.02_cal.nc INFO 2025-06-26 20:25:07,825 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:25:07,826 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.210.02_align.nc INFO 2025-06-26 20:25:07,918 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:25:07,934 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:07,949 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:07,953 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:07,968 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:08,005 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:08,011 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:08,026 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:08,038 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:08,066 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:08,078 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014210/2014.210.02 done. INFO 2025-06-26 20:25:08,078 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:25:08,080 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.210.02_1S_Gulper.txt INFO 2025-06-26 20:25:08,084 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.210.02/dorado_2014.210.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:25:08,084 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.210.02/dorado_2014.210.02_processing.log /Volumes/AUVCTD/surveys/2014/netcdf