Execution of AUVprocess_main version 1.87 at 2018-06-06T22:30:41Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2011, ['157.01'], '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: 2011.157.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/ 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/2011/2011157/2011.157.01/navigation.nc') Creating vector time with 247478 elements. Creating vector mPos_x with 247478 elements. Creating vector time with 247478 elements. Creating vector mPos_y with 247478 elements. Creating vector time with 247478 elements. Creating vector mDepth with 247478 elements. Creating vector time with 247478 elements. Creating vector mGpsNorth with 247478 elements. Creating vector time with 247478 elements. Creating vector mGpsEast with 247478 elements. Creating vector time with 247478 elements. Creating vector mGpsValid with 247478 elements. Creating vector time with 247478 elements. Creating vector mPhi with 247478 elements. Creating vector time with 247478 elements. Creating vector mTheta with 247478 elements. Creating vector time with 247478 elements. Creating vector mPsi with 247478 elements. Creating vector time with 247478 elements. Creating vector mOmega_x with 247478 elements. Creating vector time with 247478 elements. Creating vector mOmega_y with 247478 elements. Creating vector time with 247478 elements. Creating vector mOmega_z with 247478 elements. Creating vector time with 247478 elements. Creating vector mPsaRange with 247478 elements. Creating vector time with 247478 elements. Creating vector mAltitude with 247478 elements. Creating vector time with 247478 elements. Creating vector mDvlAltitude with 247478 elements. Creating vector time with 247478 elements. Creating vector mEchoAltitude with 247478 elements. Creating vector time with 247478 elements. Creating vector mEchoHorizRange with 247478 elements. Creating vector time with 247478 elements. Creating vector mEchoAltitudeLast with 247478 elements. Creating vector time with 247478 elements. Creating vector mEchoHorizRangeLast with 247478 elements. Creating vector time with 247478 elements. Creating vector mEchoNumOfPings with 247478 elements. Creating vector time with 247478 elements. Creating vector mWaterSpeed with 247478 elements. Creating vector time with 247478 elements. Creating vector mDvlValid with 247478 elements. Creating vector time with 247478 elements. Creating vector mDvlNewData with 247478 elements. Creating vector time with 247478 elements. Creating vector mDeltaT with 247478 elements. Creating vector time with 247478 elements. Creating vector nfix with 247478 elements. Creating vector time with 247478 elements. Creating vector efix with 247478 elements. Creating vector time with 247478 elements. Creating vector filter_north with 247478 elements. Creating vector time with 247478 elements. Creating vector filter_east with 247478 elements. Creating vector time with 247478 elements. Creating vector filter_depth with 247478 elements. Creating vector time with 247478 elements. Creating vector north_current with 247478 elements. Creating vector time with 247478 elements. Creating vector east_current with 247478 elements. Creating vector time with 247478 elements. Creating vector speed_bias with 247478 elements. Creating vector time with 247478 elements. Creating vector heading_bias with 247478 elements. Creating vector time with 247478 elements. Creating vector latitude with 247478 elements. Creating vector time with 247478 elements. Creating vector longitude with 247478 elements. Creating vector time with 247478 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/navigation.nc'); processNav(): median of positive valued depths = 833.8014 processNav(): Finding depths less than 5836.6099 and times > 0 processNav(): length(Nav.depth) = 247478 processNav(): length(gindx) = 247478 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/2011/2011157/2011.157.01/gps.nc') Creating vector time with 97 elements. Creating vector hours with 97 elements. Creating vector time with 97 elements. Creating vector minutes with 97 elements. Creating vector time with 97 elements. Creating vector seconds with 97 elements. Creating vector time with 97 elements. Creating vector centiSeconds with 97 elements. Creating vector time with 97 elements. Creating vector latitude with 97 elements. Creating vector time with 97 elements. Creating vector longitude with 97 elements. Creating vector time with 97 elements. Creating vector quality with 97 elements. Creating vector time with 97 elements. Creating vector numberOfSatellites with 97 elements. Creating vector time with 97 elements. Creating vector hdop with 97 elements. Creating vector time with 97 elements. Creating vector antennaHeight with 97 elements. Creating vector time with 97 elements. Creating vector geoHeight with 97 elements. Creating vector time with 97 elements. Creating vector dgpsDataAge with 97 elements. Creating vector time with 97 elements. Creating vector dgpsRSID with 97 elements. Creating vector time with 97 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/parosci.nc') Creating vector time with 451579 elements. Creating vector depth with 451579 elements. Creating vector time with 451579 elements. Creating vector temp with 451579 elements. Creating vector time with 451579 elements. Creating vector pressure with 451579 elements. Creating vector time with 451579 elements. Creating vector temp_period with 451579 elements. Creating vector time with 451579 elements. Creating vector pres_period with 451579 elements. Creating vector time with 451579 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = 0.028505 max(Depth.data) = 883.9751 Found 442075 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = 0.028505 max(Depth.data) = 299.9945 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/2011/2011157/2011.157.01/hydroscatlog.nc') Creating vector time with 197948 elements. Creating vector Seconds with 197948 elements. Creating vector time with 197948 elements. Creating vector HundrethsOfSeconds with 197948 elements. Creating vector time with 197948 elements. Creating vector Snorm1 with 197948 elements. Creating vector time with 197948 elements. Creating vector Snorm2 with 197948 elements. Creating vector time with 197948 elements. Creating vector Snorm3 with 197948 elements. Creating vector time with 197948 elements. Creating vector Gain_Status_1 with 197948 elements. Creating vector time with 197948 elements. Creating vector Gain_Status_2 with 197948 elements. Creating vector time with 197948 elements. Creating vector Gain_Status_3 with 197948 elements. Creating vector time with 197948 elements. Creating vector RawDepthValue with 197948 elements. Creating vector time with 197948 elements. Creating vector RawTempValue with 197948 elements. Creating vector time with 197948 elements. Creating vector Temperature with 197948 elements. Creating vector time with 197948 elements. Creating vector ErrorValue with 197948 elements. Creating vector time with 197948 elements. Creating vector bb470 with 197948 elements. Creating vector time with 197948 elements. Creating vector bb676 with 197948 elements. Creating vector time with 197948 elements. Creating vector fl676u with 197948 elements. Creating vector time with 197948 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/ctdDriver.nc') Creating vector time with 197950 elements. Creating vector conductivity with 197950 elements. Creating vector time with 197950 elements. Creating vector temperature with 197950 elements. Creating vector time with 197950 elements. Creating vector cond_frequency with 197950 elements. Creating vector time with 197950 elements. Creating vector temp_frequency with 197950 elements. Creating vector time with 197950 elements. Creating vector spare with 197950 elements. Creating vector time with 197950 elements. Creating vector humidity with 197950 elements. Creating vector time with 197950 elements. Creating vector flow1 with 197950 elements. Creating vector time with 197950 elements. Creating vector SecondaryDissolvedO2 with 197950 elements. Creating vector time with 197950 elements. Creating vector dissolvedO2 with 197950 elements. Creating vector time with 197950 elements. Creating vector salinity with 197950 elements. Creating vector time with 197950 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/ctdDriver2.nc') Creating vector time with 197951 elements. Creating vector conductivity with 197951 elements. Creating vector time with 197951 elements. Creating vector temperature with 197951 elements. Creating vector time with 197951 elements. Creating vector cond_frequency with 197951 elements. Creating vector time with 197951 elements. Creating vector temp_frequency with 197951 elements. Creating vector time with 197951 elements. Creating vector flow2 with 197951 elements. Creating vector time with 197951 elements. Creating vector spare with 197951 elements. Creating vector time with 197951 elements. Creating vector salinity with 197951 elements. Creating vector time with 197951 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/isuslog.nc') Creating vector time with 49035 elements. Creating vector isusNitrate with 49035 elements. Creating vector time with 49035 elements. Creating vector isusTemp with 49035 elements. Creating vector time with 49035 elements. Creating vector isusQuality with 49035 elements. Creating vector time with 49035 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/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) In reprocess_surveys (line 1072)] [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) In reprocess_surveys (line 1072)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/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/2011/2011157/2011.157.01/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_2011.157.01.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_2011.157.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... matchDVLtoGPS(): No underwater portion identified with tDiffCrit = 720 matchDVLtoGPS(): almostMaxDiff = 0.16992 not big enough. Probably stayed at surface the whole mission. Looping over 0 segments. Current plot held [Warning: Ignoring extra legend entries.] [> In legend>set_children_and_strings (line 646) In legend>make_legend (line 316) In legend (line 259) In create_data_products (line 82) In build_auv_survey (line 522) In AUVprocess_main (line 255) In reprocess_surveys (line 1072)] Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01.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 = 6 Gridding with nix = 18, iZ = 1765 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 No valid data for gT cvarname = gS No valid data for gS cvarname = gO No valid data for gO cvarname = gN No valid data for gN cvarname = gF No valid data for gF cvarname = gB470 No valid data for gB470 cvarname = gB676 No valid data for 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 97 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: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Perhaps grdtrack could not be found in the search path. Setting ocean depths to 4000m for the track. Executing: /bin/rm -f ../results/2011157_GulperTimes.txt && touch ../results/2011157_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/2011/2011157/2011.157.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2011/2011157/2011.157.01/syslog -startEsecs 1307341104.4034 -surveyName Dorado389_2011_157_01_157_01 >> ../results/2011157_GulperTimes.txt Executing: removeGulpDups.py ../results/2011157_GulperTimes.txt Bottle 0 time is 48641.1218 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 1 time is 48983.1218 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 2 time is 49035.9208 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 3 time is 49194.1218 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 4 time is 49246.1218 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 5 time is 49299.1218 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 6 time is 49352.1218 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 7 time is 49405.1218 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_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 [Warning: Contour not rendered for non-finite ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 120) In build_auv_survey (line 522) In AUVprocess_main (line 255) In reprocess_surveys (line 1072)] Failed to plot_sections. ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... [Warning: P-file /mbari/matlab/toolbox/matlab/graph2d/subplot.p is older than MATLAB file /mbari/matlab/toolbox/matlab/graph2d/subplot.m. /mbari/matlab/toolbox/matlab/graph2d/subplot.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In plot_survey_stats (line 47) In create_data_products (line 133) In build_auv_survey (line 522) In AUVprocess_main (line 255) In reprocess_surveys (line 1072)] Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_2column.png... Tried, but failed to copy to /mbari/AUVCTD/surveys/2011/images/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_2column.png’: No such file or directory Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_biolume.png... Tried, but failed to copy to /mbari/AUVCTD/surveys/2011/images/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_biolume.png’: No such file or directory Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_lopc.png... Tried, but failed to copy to /mbari/AUVCTD/surveys/2011/images/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_lopc.png’: No such file or directory Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Temperature.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Salinity.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Oxygen.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Optical_Backscatter_470_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Optical_Backscatter_470_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Optical_Backscatter_676_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Optical_Backscatter_676_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Chlorophyll_Fluorescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2011_157_01_157_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01.kml... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_157_01_157_01_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 419) In build_auv_survey (line 522) In AUVprocess_main (line 255) In reprocess_surveys (line 1072)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 4 NaNs found in bbpRed. Interpolating anyway. Encountered 48667 NaN values in array of lon that is 48684 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: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Setting bottom depth to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01.txt... Copied to /mbari/AUVCTD/surveys/2011/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2011/odv/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 4 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2011/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_2011_157_01_157_01.nc... Copied to /mbari/AUVCTD/surveys/2011/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_157_01_157_01.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2011_157_01_157_01 processed" mccann@mbari.org < mail_Dorado389_2011_157_01_157_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.157.01.mat Processing time: 126 seconds