INFO 2025-06-26 20:18:01,328 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 20:18:01,328 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:18:01,328 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.103.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:18:01,328 process.py download_process():165 [1] Download and processing steps for 2014.103.01 INFO 2025-06-26 20:18:01,328 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014103/2014.103.01 INFO 2025-06-26 20:18:01,329 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014103/2014.103.01 to /data/auv_data/dorado/missionlogs/2014.103.01 INFO 2025-06-26 20:18:04,736 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.103.01 INFO 2025-06-26 20:18:04,736 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/ctdDriver.log (4051878 bytes) INFO 2025-06-26 20:18:05,032 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/ctdDriver2.log (4051871 bytes) INFO 2025-06-26 20:18:05,320 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/gps.log (49892 bytes) INFO 2025-06-26 20:18:05,334 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/hydroscatlog.log (3550870 bytes) INFO 2025-06-26 20:18:05,696 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/navigation.log (15169122 bytes) INFO 2025-06-26 20:18:06,769 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/isuslog.log (262357 bytes) INFO 2025-06-26 20:18:06,806 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/parosci.log (4984598 bytes) INFO 2025-06-26 20:18:07,208 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.103.01/parosci.log: [4208 4209 4210] INFO 2025-06-26 20:18:07,220 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/tailCone.log (2539003 bytes) INFO 2025-06-26 20:18:07,530 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/biolume.log (2956862 bytes) INFO 2025-06-26 20:18:07,819 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:18:07,965 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.23 seconds INFO 2025-06-26 20:18:07,966 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.01/lopc.bin (32653960 bytes) INFO 2025-06-26 20:18:07,966 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:18:07 2025 INFO 2025-06-26 20:18:07,966 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.103.01/parosci.nc INFO 2025-06-26 20:18:07,966 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:18:07,966 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.103.01/parosci.nc INFO 2025-06-26 20:18:07,969 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397414649.1, sensor_off_time = 1397425224.6 INFO 2025-06-26 20:18:07,970 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10575 seconds. Expecting to read 21150 L frames from the lopc.bin file. INFO 2025-06-26 20:18:07,970 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21150 records from the lopc.bin file. INFO 2025-06-26 20:18:08,101 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-13 18:44:09 Z and endTime = 2014-04-13 21:40:24 Z with 21150 records expected to be read from lopc.bin INFO 2025-06-26 20:18:08,101 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.103.01/lopc.bin INFO 2025-06-26 20:18:08,101 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.103.01/lopc.nc INFO 2025-06-26 20:18:08,101 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.103.01/lopc.nc INFO 2025-06-26 20:18:08,102 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.103.01 INFO 2025-06-26 20:18:08,102 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:18:08,105 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:18:08,196 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:18:08,196 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:18:08,196 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:18:08,461 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:18:08,462 process.py calibrate():227 [1] Calibration steps for 2014.103.01 INFO 2025-06-26 20:18:08,590 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 20:18:08,592 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:18:09,172 calibrate.py _nudge_pos():1806 [1] 100: 0.040 -0.0001363 0.0000826 700 2.33 -9.029 6.569 2014-04-13T18:48:04.185636864 INFO 2025-06-26 20:18:09,712 calibrate.py _nudge_pos():1806 [1] 157: 0.050 0.0007593 -0.0003407 7460 24.86 4.713 -2.539 2014-04-13T19:13:52.179591936 INFO 2025-06-26 20:18:10,237 calibrate.py _nudge_pos():1806 [1] 213: 0.050 0.0006656 -0.0004642 10225 34.08 3.015 -2.524 2014-04-13T19:48:52.185731584 INFO 2025-06-26 20:18:10,762 calibrate.py _nudge_pos():1806 [1] 270: 0.050 0.0001061 -0.0001621 6980 23.26 0.704 -1.291 2014-04-13T20:13:04.186262784 INFO 2025-06-26 20:18:11,251 calibrate.py _nudge_pos():1806 [1] 323: 0.060 -0.0028711 -0.0004650 9610 32.03 -13.843 -2.690 2014-04-13T20:45:58.181035008 INFO 2025-06-26 20:18:11,801 calibrate.py _nudge_pos():1806 [1] 381: 0.060 -0.0017742 -0.0007947 7245 24.15 -11.349 -6.098 2014-04-13T21:11:04.187866368 INFO 2025-06-26 20:18:12,293 calibrate.py _nudge_pos():1806 [1] 432: 0.070 -0.0012529 -0.0007997 7310 24.36 -7.945 -6.083 2014-04-13T21:36:16.184287488 INFO 2025-06-26 20:18:14,652 calibrate.py _nudge_pos():1862 [1] 634: - - - 2 0.00 - - INFO 2025-06-26 20:18:14,652 calibrate.py _nudge_pos():1868 [1] Points in final series = 52662 INFO 2025-06-26 20:18:16,710 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:18:17,116 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:18:17,441 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:18:17,442 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.103.01/ctd1.nc INFO 2025-06-26 20:18:17,443 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:18:17,444 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 20:18:17,444 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:18:17,823 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:18:18,136 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:18:18,138 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.103.01/ctd2.nc INFO 2025-06-26 20:18:18,140 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:18:18,140 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 20:18:18,140 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:18:18,161 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:18:18,678 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69] INFO 2025-06-26 20:18:18,772 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:18:28,281 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.103.01 ERROR 2025-06-26 20:18:28,281 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.103.01 INFO 2025-06-26 20:18:28,325 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_cal.nc INFO 2025-06-26 20:18:28,420 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 20:18:28,425 process.py align():251 [1] Alignment steps for 2014.103.01 INFO 2025-06-26 20:18:28,457 align.py process_cal():139 [1] Processing dorado_2014.103.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.103.01 INFO 2025-06-26 20:18:28,475 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:18:28,478 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:18:28,518 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:18:28,522 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:18:28,564 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:18:28,568 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:18:28,591 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:18:28,591 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:18:28,607 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:18:28,610 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:18:28,650 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,652 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,687 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,690 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,725 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,728 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,762 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,765 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,801 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,804 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,838 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,841 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,877 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,880 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,914 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,917 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,953 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,956 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:28,990 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:28,993 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,029 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,032 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,067 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,070 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,105 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,108 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,143 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,146 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,182 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,185 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,220 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,223 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,259 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,262 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,299 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,304 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,346 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,349 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,385 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,388 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,424 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,427 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,463 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:18:29,466 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:18:29,510 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:18:29,543 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:18:29,577 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:18:29,612 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:18:29,647 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:18:29,699 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:18:29,966 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:18:29,995 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_align.nc INFO 2025-06-26 20:18:30,096 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 20:18:30,098 process.py resample():273 [1] Resampling steps for 2014.103.01 INFO 2025-06-26 20:18:30,099 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:18:30,127 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_align.nc mission netCDF file INFO 2025-06-26 20:18:30,132 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_align.nc mission netCDF file INFO 2025-06-26 20:18:30,134 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-13T18:44:52.398775040 to 2014-04-13T21:40:24.587270656 (0 days 00:00:00.079994880 before mission_end) INFO 2025-06-26 20:18:30,135 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-13T18:44:14.681358848 to 2014-04-13T21:40:24.497276928 (0 days 00:00:00.169988608 before mission_end) INFO 2025-06-26 20:18:30,136 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-13T18:44:34.899973888 to 2014-04-13T21:40:24.667265536 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:18:30,138 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-13T18:44:35.129958144 to 2014-04-13T21:40:24.647266560 (0 days 00:00:00.019998976 before mission_end) INFO 2025-06-26 20:18:30,139 resample.py get_mission_start_end():1145 [1] isus : 2014-04-13T18:45:22.096740608 to 2014-04-13T21:40:24.567272192 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 20:18:30,140 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-13T18:44:06.711870720 to 2014-04-13T21:40:23.237328896 (0 days 00:00:01.429936640 before mission_end) INFO 2025-06-26 20:18:30,142 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-13T18:44:07.881824768 to 2014-04-13T21:40:24.647266560 (0 days 00:00:00.019998976 before mission_end) INFO 2025-06-26 20:18:30,142 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_align.nc mission netCDF file INFO 2025-06-26 20:18:30,143 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,268 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,291 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,313 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,337 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,358 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,379 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,399 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,418 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,436 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,455 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,474 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,492 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,510 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,528 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,546 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,564 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,583 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,603 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,623 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,642 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,661 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,681 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,700 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,720 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,731 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,743 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,753 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,763 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,773 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:30,776 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:18:30,776 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:18:31,149 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:18:31,217 resample.py add_biolume_proxies():633 [1] Zero flow values found: 10578 of 10578 - replaced with 350 ml/s INFO 2025-06-26 20:18:31,217 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:18:31,255 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:18:31,272 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:18:31,288 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:18:31,288 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:18:31,315 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:18:31,483 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_1S.nc INFO 2025-06-26 20:18:33,592 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:18:43,290 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.103.01/dorado_2014.103.01_1S_Gulper.txt INFO 2025-06-26 20:18:43,291 process.py archive():337 [1] Archiving steps for 2014.103.01 INFO 2025-06-26 20:18:43,291 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:18:43,292 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:18:43,293 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.103.01_1S.nc INFO 2025-06-26 20:18:43,308 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:18:43,309 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.103.01_cal.nc INFO 2025-06-26 20:18:43,380 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:18:43,381 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.103.01_align.nc INFO 2025-06-26 20:18:43,477 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:18:43,493 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,508 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,512 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,525 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,563 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,569 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,586 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,599 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,627 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,633 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.01 done. INFO 2025-06-26 20:18:43,633 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:18:43,634 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.103.01_1S_Gulper.txt INFO 2025-06-26 20:18:43,638 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.103.01/dorado_2014.103.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:18:43,639 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.01/dorado_2014.103.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf