Execution of AUVprocess_main version 1.86 at 2018-06-02T01:43:56Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2003, ['234.02'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2003.234.02 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/navigation.nc') Creating vector time with 75694 elements. Creating vector mPos_x with 75694 elements. Creating vector time with 75694 elements. Creating vector mPos_y with 75694 elements. Creating vector time with 75694 elements. Creating vector mDepth with 75694 elements. Creating vector time with 75694 elements. Creating vector mGpsNorth with 75694 elements. Creating vector time with 75694 elements. Creating vector mGpsEast with 75694 elements. Creating vector time with 75694 elements. Creating vector mGpsValid with 75694 elements. Creating vector time with 75694 elements. Creating vector mPhi with 75694 elements. Creating vector time with 75694 elements. Creating vector mTheta with 75694 elements. Creating vector time with 75694 elements. Creating vector mPsi with 75694 elements. Creating vector time with 75694 elements. Creating vector mOmega_x with 75694 elements. Creating vector time with 75694 elements. Creating vector mOmega_y with 75694 elements. Creating vector time with 75694 elements. Creating vector mOmega_z with 75694 elements. Creating vector time with 75694 elements. Creating vector mPsaRange with 75694 elements. Creating vector time with 75694 elements. Creating vector mAltitude with 75694 elements. Creating vector time with 75694 elements. Creating vector mWaterSpeed with 75694 elements. Creating vector time with 75694 elements. Creating vector nfix with 75694 elements. Creating vector time with 75694 elements. Creating vector efix with 75694 elements. Creating vector time with 75694 elements. Creating vector filter_north with 75694 elements. Creating vector time with 75694 elements. Creating vector filter_east with 75694 elements. Creating vector time with 75694 elements. Creating vector filter_depth with 75694 elements. Creating vector time with 75694 elements. Creating vector north_current with 75694 elements. Creating vector time with 75694 elements. Creating vector east_current with 75694 elements. Creating vector time with 75694 elements. Creating vector speed_bias with 75694 elements. Creating vector time with 75694 elements. Creating vector heading_bias with 75694 elements. Creating vector time with 75694 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/navigation.nc'); processNav(): median of positive valued depths = 58.6591 processNav(): Finding depths less than 410.614 and times > 0 processNav(): length(Nav.depth) = 75694 processNav(): length(gindx) = 75694 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/gps.nc') Creating vector time with 516 elements. Creating vector UTCTime with 516 elements. Creating vector time with 516 elements. Creating vector latitude with 516 elements. Creating vector time with 516 elements. Creating vector longitude with 516 elements. Creating vector time with 516 elements. Creating vector quality with 516 elements. Creating vector time with 516 elements. Creating vector numberOfSatellites with 516 elements. Creating vector time with 516 elements. Creating vector hdop with 516 elements. Creating vector time with 516 elements. Creating vector antennaHeight with 516 elements. Creating vector time with 516 elements. Creating vector geoHeight with 516 elements. Creating vector time with 516 elements. Creating vector dgpsDataAge with 516 elements. Creating vector time with 516 elements. Creating vector dgpsRSID with 516 elements. Creating vector time with 516 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/parosci.nc') Creating vector time with 75798 elements. Creating vector depth with 75798 elements. Creating vector time with 75798 elements. Creating vector temp with 75798 elements. Creating vector time with 75798 elements. Creating vector pressure with 75798 elements. Creating vector time with 75798 elements. Creating vector temp_period with 75798 elements. Creating vector time with 75798 elements. Creating vector pres_period with 75798 elements. Creating vector time with 75798 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.12423 max(Depth.data) = 251.0632 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.12423 max(Depth.data) = 251.0632 Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/hydroscatlog.nc') Creating vector time with 60593 elements. Creating vector Seconds with 60593 elements. Creating vector time with 60593 elements. Creating vector HundrethsOfSeconds with 60593 elements. Creating vector time with 60593 elements. Creating vector Snorm1 with 60593 elements. Creating vector time with 60593 elements. Creating vector Snorm2 with 60593 elements. Creating vector time with 60593 elements. Creating vector Snorm3 with 60593 elements. Creating vector time with 60593 elements. Creating vector Gain_Status_1 with 60593 elements. Creating vector time with 60593 elements. Creating vector Gain_Status_2 with 60593 elements. Creating vector time with 60593 elements. Creating vector Gain_Status_3 with 60593 elements. Creating vector time with 60593 elements. Creating vector RawDepthValue with 60593 elements. Creating vector time with 60593 elements. Creating vector RawTempValue with 60593 elements. Creating vector time with 60593 elements. Creating vector Temperature with 60593 elements. Creating vector time with 60593 elements. Creating vector ErrorValue with 60593 elements. Creating vector time with 60593 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ctdDriver.nc') Creating vector time with 60558 elements. Creating vector conductivity with 60558 elements. Creating vector time with 60558 elements. Creating vector temperature with 60558 elements. Creating vector time with 60558 elements. Creating vector cond_frequency with 60558 elements. Creating vector time with 60558 elements. Creating vector temp_frequency with 60558 elements. Creating vector time with 60558 elements. Creating vector spare with 60558 elements. Creating vector time with 60558 elements. Creating vector humidity with 60558 elements. Creating vector time with 60558 elements. Creating vector flow1 with 60558 elements. Creating vector time with 60558 elements. Creating vector OBS with 60558 elements. Creating vector time with 60558 elements. Creating vector dissolvedO2 with 60558 elements. Creating vector time with 60558 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ctdDriver2.nc') Creating vector time with 60556 elements. Creating vector conductivity with 60556 elements. Creating vector time with 60556 elements. Creating vector temperature with 60556 elements. Creating vector time with 60556 elements. Creating vector cond_frequency with 60556 elements. Creating vector time with 60556 elements. Creating vector temp_frequency with 60556 elements. Creating vector time with 60556 elements. Creating vector flow2 with 60556 elements. Creating vector time with 60556 elements. Creating vector spare with 60556 elements. Creating vector time with 60556 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/isuslog.nc') Creating vector time with 9121 elements. Creating vector isusNitrate with 9121 elements. Creating vector time with 9121 elements. Creating vector isusTemp with 9121 elements. Creating vector time with 9121 elements. Creating vector isusQuality with 9121 elements. Creating vector time with 9121 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/biolume.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/biolume.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/biolume.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/biolume.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. Could not read from biolume.nc returning NaNs for fields. Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.234.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.234.02.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 6 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 46 Gridding with nix = 138, iZ = 499 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp470 bbp676 fl676_uncorr N BL Only one good point or fewer - NaNing the gBL array. BLflow Only one good point or fewer - NaNing the gBLflow array. LOPC Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB470 cvarname = gB676 cvarname = gBL No valid data for gBL cvarname = gBLflow No valid data for gBLflow cvarname = gLOPCcount No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 75586 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 75586 points from grid Monterey25.grd (2876 x 2447) Executing: /bin/rm -f ../results/2003234_GulperTimes.txt && touch ../results/2003234_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003234/2003.234.02/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003234/2003.234.02/syslog -startEsecs 1061569954.1727 -surveyName Dorado389_2003_234_02_234_02 >> ../results/2003234_GulperTimes.txt Executing: removeGulpDups.py ../results/2003234_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_gridded.mat outvarstr = 'gF gT gN gS gD gO gB470 gB676 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_2column.png Elapsed time to save image: 9 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB470 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB676 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_biolume.png Elapsed time to save image: 31 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_lopc.png Elapsed time to save image: 9 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_2column.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_biolume.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_lopc.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing KML files ... KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Optical_Backscatter_470_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Optical_Backscatter_470_nm.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Optical_Backscatter_676_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Optical_Backscatter_676_nm.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2003_234_02_234_02.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.kml... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_234_02_234_02_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 13 NaN values in array of lon that is 9121 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 9108 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 9108 are not equal to number of Lat lon points = 9121 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.txt... Copied to /mbari/AUVCTD/surveys/2003/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2003/odv/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_decim.nc... Copied to /mbari/AUVCTD/surveys/2003/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.nc... Copied to /mbari/AUVCTD/surveys/2003/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02_gridded.mat... Copied to /mbari/AUVCTD/surveys/2003/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_234_02_234_02.mat... Copied to /mbari/AUVCTD/surveys/2003/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2003_234_02_234_02 processed" mccann@mbari.org < mail_Dorado389_2003_234_02_234_02.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.234.02.mat Processing time: 103 seconds