INFO 2025-06-26 20:13:01,082 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 20:13:01,082 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Spring 2014 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:13:01,082 process.py process_mission():449 [1] Processing SIMZ Spring 2014 mission 2014.050.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:13:01,082 process.py download_process():165 [1] Download and processing steps for 2014.050.01 INFO 2025-06-26 20:13:01,082 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014050/2014.050.01 INFO 2025-06-26 20:13:01,083 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014050/2014.050.01 to /data/auv_data/dorado/missionlogs/2014.050.01 INFO 2025-06-26 20:13:04,542 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.050.01 INFO 2025-06-26 20:13:04,542 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/ctdDriver.log (6237606 bytes) INFO 2025-06-26 20:13:04,982 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/ctdDriver2.log (6237599 bytes) INFO 2025-06-26 20:13:05,440 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/gps.log (69188 bytes) INFO 2025-06-26 20:13:05,457 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/hydroscatlog.log (5462794 bytes) INFO 2025-06-26 20:13:06,012 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/navigation.log (23363010 bytes) INFO 2025-06-26 20:13:07,683 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/parosci.log (7672454 bytes) INFO 2025-06-26 20:13:08,334 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/tailCone.log (3904987 bytes) INFO 2025-06-26 20:13:08,809 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/biolume.log (4546694 bytes) INFO 2025-06-26 20:13:09,250 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:13:09,473 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.93 seconds INFO 2025-06-26 20:13:09,474 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.050.01/lopc.bin (32270649 bytes) INFO 2025-06-26 20:13:09,474 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:13:09 2025 INFO 2025-06-26 20:13:09,474 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.050.01/parosci.nc INFO 2025-06-26 20:13:09,474 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:13:09,474 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.050.01/parosci.nc INFO 2025-06-26 20:13:09,477 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1392833641.8, sensor_off_time = 1392849910.4 INFO 2025-06-26 20:13:09,478 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 16268 seconds. Expecting to read 32536 L frames from the lopc.bin file. INFO 2025-06-26 20:13:09,478 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 32536 records from the lopc.bin file. INFO 2025-06-26 20:13:09,669 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-02-19 18:14:01 Z and endTime = 2014-02-19 22:45:10 Z with 32536 records expected to be read from lopc.bin INFO 2025-06-26 20:13:09,670 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.050.01/lopc.bin INFO 2025-06-26 20:13:09,670 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.050.01/lopc.nc INFO 2025-06-26 20:13:09,670 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.050.01/lopc.nc INFO 2025-06-26 20:13:09,670 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.050.01 INFO 2025-06-26 20:13:09,671 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:13:09,673 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:13:09,710 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:13:09,710 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:13:09,710 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:13:14,177 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:13:14,178 process.py calibrate():227 [1] Calibration steps for 2014.050.01 INFO 2025-06-26 20:13:14,347 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 20:13:14,349 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:13:15,016 calibrate.py _nudge_pos():1806 [1] 109: 0.060 0.0000517 0.0036160 8780 29.26 0.262 22.897 2014-02-19T18:45:04.246910208 INFO 2025-06-26 20:13:15,405 calibrate.py _nudge_pos():1806 [1] 151: 0.060 0.0000264 -0.0000072 20 0.06 61.875 -20.953 2014-02-19T18:45:49.243827456 INFO 2025-06-26 20:13:15,452 calibrate.py _nudge_pos():1806 [1] 156: 0.060 0.0021937 0.0044818 9145 30.48 10.668 27.246 2014-02-19T19:16:22.248258048 INFO 2025-06-26 20:13:15,906 calibrate.py _nudge_pos():1806 [1] 205: 0.060 -0.0003859 -0.0004854 13525 45.08 -1.269 -1.995 2014-02-19T20:02:16.249596160 INFO 2025-06-26 20:13:16,407 calibrate.py _nudge_pos():1806 [1] 259: 0.070 -0.0000316 0.0002865 1295 4.31 -1.086 12.308 2014-02-19T20:07:28.248222720 INFO 2025-06-26 20:13:17,414 calibrate.py _nudge_pos():1806 [1] 368: 0.070 0.0009211 0.0000508 4615 15.38 8.880 0.612 2014-02-19T20:24:40.247525888 INFO 2025-06-26 20:13:17,903 calibrate.py _nudge_pos():1806 [1] 420: 0.070 0.0007306 -0.0004022 4695 15.65 6.922 -4.764 2014-02-19T20:41:10.249706240 INFO 2025-06-26 20:13:18,298 calibrate.py _nudge_pos():1806 [1] 462: 0.080 0.0003427 -0.0009846 6635 22.11 2.297 -8.251 2014-02-19T21:03:58.245991936 INFO 2025-06-26 20:13:18,732 calibrate.py _nudge_pos():1806 [1] 508: 0.090 0.0003691 -0.0008279 4455 14.85 3.685 -10.333 2014-02-19T21:19:34.241871872 INFO 2025-06-26 20:13:18,968 calibrate.py _nudge_pos():1806 [1] 533: 0.080 -0.0000122 -0.0008721 3720 12.40 -0.146 -13.035 2014-02-19T21:32:22.249260032 INFO 2025-06-26 20:13:19,310 calibrate.py _nudge_pos():1806 [1] 569: 0.080 0.0000153 -0.0000224 20 0.06 35.721 -65.402 2014-02-19T21:33:01.246588160 INFO 2025-06-26 20:13:19,376 calibrate.py _nudge_pos():1806 [1] 576: 0.100 0.0041196 -0.0047834 17115 57.05 10.701 -15.537 2014-02-19T22:30:10.241686016 INFO 2025-06-26 20:13:20,805 calibrate.py _nudge_pos():1806 [1] 726: 0.100 0.0011138 -0.0002706 2645 8.81 18.726 -5.690 2014-02-19T22:41:28.245239808 INFO 2025-06-26 20:13:22,905 calibrate.py _nudge_pos():1862 [1] 902: - - - 1 0.00 - - INFO 2025-06-26 20:13:22,905 calibrate.py _nudge_pos():1868 [1] Points in final series = 81113 INFO 2025-06-26 20:13:23,146 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 54 of 65021 INFO 2025-06-26 20:13:23,637 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:13:24,248 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:13:24,725 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:13:24,727 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.050.01/ctd1.nc INFO 2025-06-26 20:13:24,729 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:13:24,729 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 20:13:24,729 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:13:25,302 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:13:25,781 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:13:25,783 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.050.01/ctd2.nc INFO 2025-06-26 20:13:25,784 calibrate.py _range_qc_combined_nc():898 [1] Setting 34 ctd2_salinity values to NaN INFO 2025-06-26 20:13:25,785 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 20:13:25,785 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:13:25,785 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.050.01 INFO 2025-06-26 20:13:25,798 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:13:26,536 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61] INFO 2025-06-26 20:13:26,676 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:13:41,393 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.050.01 ERROR 2025-06-26 20:13:41,393 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.050.01 INFO 2025-06-26 20:13:41,458 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_cal.nc INFO 2025-06-26 20:13:41,576 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 20:13:41,582 process.py align():251 [1] Alignment steps for 2014.050.01 INFO 2025-06-26 20:13:41,617 align.py process_cal():139 [1] Processing dorado_2014.050.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.050.01 INFO 2025-06-26 20:13:41,641 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:13:41,645 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:13:41,705 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:13:41,711 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:13:41,770 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:13:41,774 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:13:41,808 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:13:41,808 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:13:41,830 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:13:41,834 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:13:41,890 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:41,894 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:41,943 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:41,948 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:41,998 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,002 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,053 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,057 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,109 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,113 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,162 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,166 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,216 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,220 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,268 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,273 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,323 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,327 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,376 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,380 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,430 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,434 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,485 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,489 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,540 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,544 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,593 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,597 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,648 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,652 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,703 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,707 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,758 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,762 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,811 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,816 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,866 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,871 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,921 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,925 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:42,976 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:42,980 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:43,029 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.050.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:13:43,033 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:13:43,100 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:13:43,147 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:13:43,221 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:13:43,639 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:13:43,680 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_align.nc INFO 2025-06-26 20:13:43,807 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 20:13:43,809 process.py resample():273 [1] Resampling steps for 2014.050.01 INFO 2025-06-26 20:13:43,810 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:13:43,841 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_align.nc mission netCDF file INFO 2025-06-26 20:13:43,846 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_align.nc mission netCDF file INFO 2025-06-26 20:13:43,847 resample.py get_mission_start_end():1145 [1] navigation: 2014-02-19T18:14:48.061327360 to 2014-02-19T22:45:10.450017792 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 20:13:43,849 resample.py get_mission_start_end():1145 [1] hs2 : 2014-02-19T18:14:09.823946752 to 2014-02-19T22:45:10.320026368 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 20:13:43,851 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-02-19T18:14:28.752649984 to 2014-02-19T22:45:10.390021888 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 20:13:43,852 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-02-19T18:14:29.052629504 to 2014-02-19T22:45:10.460016896 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:13:43,854 resample.py get_mission_start_end():1145 [1] biolume : 2014-02-19T18:13:59.884593408 to 2014-02-19T22:45:09.700034560 (0 days 00:00:00.759982336 before mission_end) INFO 2025-06-26 20:13:43,855 resample.py get_mission_start_end():1145 [1] tailcone : 2014-02-19T18:14:01.944486656 to 2014-02-19T22:45:10.330025984 (0 days 00:00:00.129990912 before mission_end) INFO 2025-06-26 20:13:43,856 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_align.nc mission netCDF file INFO 2025-06-26 20:13:43,857 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,039 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,072 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,104 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,136 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,165 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,192 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,219 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,245 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,270 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,295 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,321 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,346 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,372 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,398 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,424 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,450 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,476 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,504 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,531 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,560 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,587 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,614 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,640 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,667 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,680 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,693 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:44,698 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:13:44,698 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:13:45,259 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:13:45,364 resample.py add_biolume_proxies():633 [1] Zero flow values found: 16271 of 16271 - replaced with 350 ml/s INFO 2025-06-26 20:13:45,365 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:13:45,421 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:13:45,446 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:13:45,468 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:13:45,468 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:13:45,502 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:13:45,696 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_1S.nc INFO 2025-06-26 20:13:47,974 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:13:57,531 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.050.01/dorado_2014.050.01_1S_Gulper.txt INFO 2025-06-26 20:13:57,531 process.py archive():337 [1] Archiving steps for 2014.050.01 INFO 2025-06-26 20:13:57,531 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:13:57,531 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:13:57,533 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.050.01_1S.nc INFO 2025-06-26 20:13:57,549 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:13:57,550 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.050.01_cal.nc INFO 2025-06-26 20:13:57,666 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:13:57,667 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.050.01_align.nc INFO 2025-06-26 20:13:57,827 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:13:57,848 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:57,869 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:57,873 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:57,891 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:57,954 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:57,977 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:57,995 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:58,040 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:58,053 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014050/2014.050.01 done. INFO 2025-06-26 20:13:58,054 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:13:58,055 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.050.01_1S_Gulper.txt INFO 2025-06-26 20:13:58,059 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.050.01/dorado_2014.050.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:13:58,059 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.050.01/dorado_2014.050.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf