INFO 2025-06-26 16:35:19,611 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 16:35:19,611 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Inner-bay survey seventh - TREX lagrangian mission near M0 and stella104 drifter - ctdToUse = ctd1 INFO 2025-06-26 16:35:19,611 process.py process_mission():449 [1] Processing AUVCTD mission 2010.286.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 16:35:19,611 process.py download_process():165 [1] Download and processing steps for 2010.286.01 INFO 2025-06-26 16:35:19,611 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010286/2010.286.01 INFO 2025-06-26 16:35:19,611 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010286/2010.286.01 to /data/auv_data/dorado/missionlogs/2010.286.01 INFO 2025-06-26 16:35:20,510 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.286.01 INFO 2025-06-26 16:35:20,510 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/ctdDriver.log (286187 bytes) INFO 2025-06-26 16:35:20,538 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/ctdDriver2.log (286175 bytes) INFO 2025-06-26 16:35:20,568 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.286.01/ctdDriver2.log: [2270] INFO 2025-06-26 16:35:20,569 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/gps.log (11804 bytes) INFO 2025-06-26 16:35:20,577 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/hydroscatlog.log (269158 bytes) INFO 2025-06-26 16:35:20,612 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.286.01/hydroscatlog.log: [3088] INFO 2025-06-26 16:35:20,613 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/navigation.log (887014 bytes) INFO 2025-06-26 16:35:20,690 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/isuslog.log (18901 bytes) INFO 2025-06-26 16:35:20,696 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.286.01/isuslog.log: [1 2 3 4 5 6 7 8 9] INFO 2025-06-26 16:35:20,696 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/parosci.log (351206 bytes) INFO 2025-06-26 16:35:20,732 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/tailCone.log (190507 bytes) INFO 2025-06-26 16:35:20,763 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/biolume.log (227338 bytes) INFO 2025-06-26 16:35:20,790 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 16:35:20,804 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.29 seconds INFO 2025-06-26 16:35:20,804 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.286.01/lopc.bin (1784000 bytes) INFO 2025-06-26 16:35:20,804 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 16:35:20 2025 INFO 2025-06-26 16:35:20,804 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.286.01/parosci.nc INFO 2025-06-26 16:35:20,804 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:35:20,804 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.286.01/parosci.nc INFO 2025-06-26 16:35:20,806 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1287009995.4, sensor_off_time = 1287010797.9 INFO 2025-06-26 16:35:20,806 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 802 seconds. Expecting to read 1604 L frames from the lopc.bin file. INFO 2025-06-26 16:35:20,806 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 1604 records from the lopc.bin file. INFO 2025-06-26 16:35:20,816 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-10-13 22:46:35 Z and endTime = 2010-10-13 22:59:57 Z with 1604 records expected to be read from lopc.bin INFO 2025-06-26 16:35:20,816 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.286.01/lopc.bin INFO 2025-06-26 16:35:20,816 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.286.01/lopc.nc INFO 2025-06-26 16:35:20,817 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.286.01/lopc.nc INFO 2025-06-26 16:35:20,817 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.286.01 INFO 2025-06-26 16:35:20,817 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 16:35:20,820 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A054267 WARNING 2025-06-26 16:35:20,820 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 16:35:20,946 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 16:35:20,946 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 16:35:20,946 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 16:35:21,420 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 16:35:21,420 process.py calibrate():227 [1] Calibration steps for 2010.286.01 INFO 2025-06-26 16:35:21,490 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 16:35:21,491 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 16:35:22,194 calibrate.py _nudge_pos():1806 [1] 116: 0.150 -0.0006410 -0.0017143 3259 10.90 -8.721 -29.152 2010-10-13T22:59:22.924360704 INFO 2025-06-26 16:35:22,526 calibrate.py _nudge_pos():1862 [1] 101: - - - 0 0.00 - - INFO 2025-06-26 16:35:22,526 calibrate.py _nudge_pos():1868 [1] Points in final series = 3749 WARNING 2025-06-26 16:35:22,535 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 16:35:22,983 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:35:23,037 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 59 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:35:23,062 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 59 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:35:23,063 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.286.01/ctd1.nc INFO 2025-06-26 16:35:23,064 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 16:35:23,065 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 16:35:23,065 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:35:23,246 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 59 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:35:23,274 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 59 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:35:23,275 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.286.01/ctd2.nc INFO 2025-06-26 16:35:23,276 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 16:35:23,277 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 16:35:23,277 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:35:23,312 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 16:35:23,346 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 300 301 302 3660 3661 3662 3663 3664 3665 12840 12841 12842 12843 12844 12845 13740 13741 13742 16980 16981 16982 16983 16984 16985 16986 16987 16988 18360 18361 18362 18363 18364 18365 18900 18901 18902 18903 18904 18905 31860 31861 31862 31863 31864 31865 33780 33781 33782 37080 37081 37082 37083 37084 37085 37086 37087 37088 38820 38821 38822 38823 38824 38825 38826 38827 38828 38829 38830 38831 38832 38833 38834 38835 44400 44401 44402 44403 44404 44405 44406 44407 44408 44409 44410 44411 44412 44413 44414 44415 44416] INFO 2025-06-26 16:35:23,355 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 16:35:24,098 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2010.286.01 ERROR 2025-06-26 16:35:24,098 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.286.01 INFO 2025-06-26 16:35:24,105 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_cal.nc INFO 2025-06-26 16:35:24,296 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 16:35:24,301 process.py align():251 [1] Alignment steps for 2010.286.01 INFO 2025-06-26 16:35:24,325 align.py process_cal():139 [1] Processing dorado_2010.286.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.286.01 INFO 2025-06-26 16:35:24,330 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:35:24,332 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:35:24,344 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:35:24,346 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:35:24,356 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:35:24,357 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:35:24,363 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 16:35:24,363 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 16:35:24,367 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:35:24,369 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:35:24,379 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,381 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,391 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,393 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,403 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,404 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,414 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,416 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,426 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,427 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,437 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,439 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,449 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,451 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,461 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,463 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,473 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,475 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,485 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,487 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,497 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,499 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,509 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,511 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,521 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,523 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,533 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,534 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,545 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,547 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,558 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,559 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,570 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,572 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,582 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,584 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,595 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,597 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,607 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,609 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,620 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,622 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,632 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.286.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:35:24,634 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:35:24,648 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:35:24,661 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:35:24,674 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:35:24,688 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:35:24,703 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:35:24,719 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.88 INFO 2025-06-26 16:35:24,751 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 16:35:24,762 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_align.nc INFO 2025-06-26 16:35:24,814 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 16:35:24,816 process.py resample():273 [1] Resampling steps for 2010.286.01 INFO 2025-06-26 16:35:24,817 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 16:35:24,840 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_align.nc mission netCDF file INFO 2025-06-26 16:35:24,845 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_align.nc mission netCDF file INFO 2025-06-26 16:35:24,846 resample.py get_mission_start_end():1145 [1] navigation: 2010-10-13T22:47:25.893480704 to 2010-10-13T22:59:58.131948800 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 16:35:24,847 resample.py get_mission_start_end():1145 [1] hs2 : 2010-10-13T22:46:40.776571392 to 2010-10-13T22:59:58.091951616 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 16:35:24,849 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-10-13T22:47:34.832868352 to 2010-10-13T22:59:58.081952256 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 16:35:24,850 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-10-13T22:47:34.922862080 to 2010-10-13T22:59:58.151947520 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:35:24,852 resample.py get_mission_start_end():1145 [1] isus : 2010-10-13T22:47:41.082440192 to 2010-10-13T22:59:57.651981568 (0 days 00:00:00.499965952 before mission_end) INFO 2025-06-26 16:35:24,853 resample.py get_mission_start_end():1145 [1] biolume : 2010-10-13T22:46:34.646957056 to 2010-10-13T22:59:56.712011776 (0 days 00:00:01.439935744 before mission_end) INFO 2025-06-26 16:35:24,855 resample.py get_mission_start_end():1145 [1] tailcone : 2010-10-13T22:46:42.266469120 to 2010-10-13T22:59:57.661981184 (0 days 00:00:00.489966336 before mission_end) INFO 2025-06-26 16:35:24,856 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_align.nc mission netCDF file INFO 2025-06-26 16:35:24,856 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,893 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,904 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,913 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,922 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,932 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,941 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,950 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,958 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,966 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,973 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,981 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,988 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:24,995 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,003 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,012 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,021 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,031 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,041 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,049 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,058 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,066 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,074 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,083 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,091 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,100 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,109 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,118 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,126 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,133 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,136 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 16:35:25,136 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 16:35:25,166 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 16:35:25,175 resample.py add_biolume_proxies():633 [1] Zero flow values found: 803 of 803 - replaced with 350 ml/s INFO 2025-06-26 16:35:25,176 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 16:35:25,181 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 16:35:25,184 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 16:35:25,188 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 16:35:25,189 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 16:35:25,203 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:25,317 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_1S.nc INFO 2025-06-26 16:35:26,458 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 16:35:26,967 create_products.py gulper_odv():522 [1] Wrote 3 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.286.01/dorado_2010.286.01_1S_Gulper.txt INFO 2025-06-26 16:35:26,967 process.py archive():337 [1] Archiving steps for 2010.286.01 INFO 2025-06-26 16:35:26,967 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01, BASE_PATH = /data/auv_data INFO 2025-06-26 16:35:26,967 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 16:35:26,968 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.286.01_1S.nc INFO 2025-06-26 16:35:26,973 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:35:26,974 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.286.01_cal.nc INFO 2025-06-26 16:35:26,985 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:35:26,986 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.286.01_align.nc INFO 2025-06-26 16:35:27,000 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:35:27,008 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,014 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,019 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,024 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,032 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,036 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,041 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,046 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,054 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,058 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010286/2010.286.01 done. INFO 2025-06-26 16:35:27,058 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 16:35:27,059 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.286.01_1S_Gulper.txt INFO 2025-06-26 16:35:27,064 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.286.01/dorado_2010.286.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 16:35:27,064 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.286.01/dorado_2010.286.01_processing.log /Volumes/AUVCTD/surveys/2010/netcdf