Execution of AUVprocess_main version 1.86 at 2018-05-24T21:50:49Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2014, ['107.00'], '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: 2014.107.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/ 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/2014/2014107/2014.107.00/navigation.nc') Creating vector time with 55069 elements. Creating vector mPos_x with 55069 elements. Creating vector time with 55069 elements. Creating vector mPos_y with 55069 elements. Creating vector time with 55069 elements. Creating vector mDepth with 55069 elements. Creating vector time with 55069 elements. Creating vector mGpsNorth with 55069 elements. Creating vector time with 55069 elements. Creating vector mGpsEast with 55069 elements. Creating vector time with 55069 elements. Creating vector mGpsValid with 55069 elements. Creating vector time with 55069 elements. Creating vector mPhi with 55069 elements. Creating vector time with 55069 elements. Creating vector mTheta with 55069 elements. Creating vector time with 55069 elements. Creating vector mPsi with 55069 elements. Creating vector time with 55069 elements. Creating vector mOmega_x with 55069 elements. Creating vector time with 55069 elements. Creating vector mOmega_y with 55069 elements. Creating vector time with 55069 elements. Creating vector mOmega_z with 55069 elements. Creating vector time with 55069 elements. Creating vector mPsaRange with 55069 elements. Creating vector time with 55069 elements. Creating vector mAltitude with 55069 elements. Creating vector time with 55069 elements. Creating vector multibeamAltitude with 55069 elements. Creating vector time with 55069 elements. Creating vector mDvlAltitude with 55069 elements. Creating vector time with 55069 elements. Creating vector mEchoAltitude with 55069 elements. Creating vector time with 55069 elements. Creating vector mEchoHorizRange with 55069 elements. Creating vector time with 55069 elements. Creating vector mEchoAltitudeLast with 55069 elements. Creating vector time with 55069 elements. Creating vector mEchoHorizRangeLast with 55069 elements. Creating vector time with 55069 elements. Creating vector mEchoNumOfPings with 55069 elements. Creating vector time with 55069 elements. Creating vector nadirCnts with 55069 elements. Creating vector time with 55069 elements. Creating vector obstacleCnts with 55069 elements. Creating vector time with 55069 elements. Creating vector mWaterSpeed with 55069 elements. Creating vector time with 55069 elements. Creating vector mDvlValid with 55069 elements. Creating vector time with 55069 elements. Creating vector mDvlNewData with 55069 elements. Creating vector time with 55069 elements. Creating vector mDeltaT with 55069 elements. Creating vector time with 55069 elements. Creating vector nfix with 55069 elements. Creating vector time with 55069 elements. Creating vector efix with 55069 elements. Creating vector time with 55069 elements. Creating vector filter_north with 55069 elements. Creating vector time with 55069 elements. Creating vector filter_east with 55069 elements. Creating vector time with 55069 elements. Creating vector filter_depth with 55069 elements. Creating vector time with 55069 elements. Creating vector north_current with 55069 elements. Creating vector time with 55069 elements. Creating vector east_current with 55069 elements. Creating vector time with 55069 elements. Creating vector speed_bias with 55069 elements. Creating vector time with 55069 elements. Creating vector heading_bias with 55069 elements. Creating vector time with 55069 elements. Creating vector latitude with 55069 elements. Creating vector time with 55069 elements. Creating vector longitude with 55069 elements. Creating vector time with 55069 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/navigation.nc'); processNav(): median of positive valued depths = 22.8406 processNav(): Finding depths less than 159.8845 and times > 0 processNav(): length(Nav.depth) = 55069 processNav(): length(gindx) = 55069 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/2014/2014107/2014.107.00/gps.nc') Creating vector time with 523 elements. Creating vector hours with 523 elements. Creating vector time with 523 elements. Creating vector minutes with 523 elements. Creating vector time with 523 elements. Creating vector seconds with 523 elements. Creating vector time with 523 elements. Creating vector centiSeconds with 523 elements. Creating vector time with 523 elements. Creating vector latitude with 523 elements. Creating vector time with 523 elements. Creating vector longitude with 523 elements. Creating vector time with 523 elements. Creating vector quality with 523 elements. Creating vector time with 523 elements. Creating vector numberOfSatellites with 523 elements. Creating vector time with 523 elements. Creating vector hdop with 523 elements. Creating vector time with 523 elements. Creating vector antennaHeight with 523 elements. Creating vector time with 523 elements. Creating vector geoHeight with 523 elements. Creating vector time with 523 elements. Creating vector dgpsDataAge with 523 elements. Creating vector time with 523 elements. Creating vector dgpsRSID with 523 elements. Creating vector time with 523 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/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/2014/2014107/2014.107.00/parosci.nc') Creating vector time with 108591 elements. Creating vector depth with 108591 elements. Creating vector time with 108591 elements. Creating vector temp with 108591 elements. Creating vector time with 108591 elements. Creating vector pressure with 108591 elements. Creating vector time with 108591 elements. Creating vector temp_period with 108591 elements. Creating vector time with 108591 elements. Creating vector pres_period with 108591 elements. Creating vector time with 108591 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.25751 max(Depth.data) = 80.8595 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.25751 max(Depth.data) = 80.8595 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/2014/2014107/2014.107.00/hydroscatlog.nc') Creating vector time with 44198 elements. Creating vector Seconds with 44198 elements. Creating vector time with 44198 elements. Creating vector HundrethsOfSeconds with 44198 elements. Creating vector time with 44198 elements. Creating vector Snorm1 with 44198 elements. Creating vector time with 44198 elements. Creating vector Snorm2 with 44198 elements. Creating vector time with 44198 elements. Creating vector Snorm3 with 44198 elements. Creating vector time with 44198 elements. Creating vector Gain_Status_1 with 44198 elements. Creating vector time with 44198 elements. Creating vector Gain_Status_2 with 44198 elements. Creating vector time with 44198 elements. Creating vector Gain_Status_3 with 44198 elements. Creating vector time with 44198 elements. Creating vector RawDepthValue with 44198 elements. Creating vector time with 44198 elements. Creating vector RawTempValue with 44198 elements. Creating vector time with 44198 elements. Creating vector Temperature with 44198 elements. Creating vector time with 44198 elements. Creating vector ErrorValue with 44198 elements. Creating vector time with 44198 elements. Creating vector bb470 with 44198 elements. Creating vector time with 44198 elements. Creating vector bb676 with 44198 elements. Creating vector time with 44198 elements. Creating vector fl676u with 44198 elements. Creating vector time with 44198 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/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/2014/2014107/2014.107.00/ctdDriver.nc') Creating vector time with 44067 elements. Creating vector conductivity with 44067 elements. Creating vector time with 44067 elements. Creating vector temperature with 44067 elements. Creating vector time with 44067 elements. Creating vector cond_frequency with 44067 elements. Creating vector time with 44067 elements. Creating vector temp_frequency with 44067 elements. Creating vector time with 44067 elements. Creating vector spare with 44067 elements. Creating vector time with 44067 elements. Creating vector humidity with 44067 elements. Creating vector time with 44067 elements. Creating vector flow1 with 44067 elements. Creating vector time with 44067 elements. Creating vector CDOM with 44067 elements. Creating vector time with 44067 elements. Creating vector dissolvedO2 with 44067 elements. Creating vector time with 44067 elements. Creating vector salinity with 44067 elements. Creating vector time with 44067 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/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/2014/2014107/2014.107.00/ctdDriver2.nc') Creating vector time with 44134 elements. Creating vector conductivity with 44134 elements. Creating vector time with 44134 elements. Creating vector temperature with 44134 elements. Creating vector time with 44134 elements. Creating vector cond_frequency with 44134 elements. Creating vector time with 44134 elements. Creating vector temp_frequency with 44134 elements. Creating vector time with 44134 elements. Creating vector flow2 with 44134 elements. Creating vector time with 44134 elements. Creating vector spare with 44134 elements. Creating vector time with 44134 elements. Creating vector salinity with 44134 elements. Creating vector time with 44134 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/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/2014/2014107/2014.107.00/isuslog.nc') Creating vector time with 8566 elements. Creating vector isusNitrate with 8566 elements. Creating vector time with 8566 elements. Creating vector isusTemp with 8566 elements. Creating vector time with 8566 elements. Creating vector isusQuality with 8566 elements. Creating vector time with 8566 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/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/2014/2014107/2014.107.00/biolume.nc') Creating vector time with 10876 elements. Creating vector rrr with 10876 elements. Creating vector time with 10876 elements. Creating vector cal_striing with 10876 elements. Creating vector time with 10876 elements. Creating vector avg_biolume with 10876 elements. Creating vector time with 10876 elements. Creating vector pump with 10876 elements. Creating vector time with 10876 elements. Creating vector system_voltage with 10876 elements. Creating vector time with 10876 elements. Creating vector flow with 10876 elements. Creating vector time with 10876 elements. Creating vector HV with 10876 elements. Creating vector time with 10876 elements. Creating vector reserved with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_0 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_1 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_2 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_3 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_4 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_5 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_6 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_7 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_8 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_9 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_10 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_11 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_12 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_13 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_14 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_15 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_16 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_17 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_18 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_19 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_20 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_21 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_22 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_23 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_24 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_25 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_26 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_27 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_28 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_29 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_30 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_31 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_32 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_33 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_34 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_35 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_36 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_37 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_38 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_39 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_40 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_41 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_42 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_43 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_44 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_45 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_46 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_47 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_48 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_49 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_50 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_51 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_52 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_53 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_54 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_55 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_56 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_57 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_58 with 10876 elements. Creating vector time with 10876 elements. Creating vector raw_59 with 10876 elements. Creating vector time with 10876 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/biolume.nc'); 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/2014/2014107/2014.107.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (772 x 994) with 767368 elements. Creating vector time with 772 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (772 x 994) with 767368 elements. Creating vector time with 772 elements. Creating vector bin with 994 elements. Creating matrix countList (772 x 994) with 767368 elements. Creating vector time with 772 elements. Creating vector bin with 994 elements. Creating vector LCcount with 772 elements. Creating vector time with 772 elements. Creating vector transCount with 772 elements. Creating vector time with 772 elements. Creating vector nonTransCount with 772 elements. Creating vector time with 772 elements. Creating vector ai_mean with 772 elements. Creating vector time with 772 elements. Creating vector ai_min with 772 elements. Creating vector time with 772 elements. Creating vector ai_max with 772 elements. Creating vector time with 772 elements. Creating vector ai_std with 772 elements. Creating vector time with 772 elements. Creating vector esd_mean with 772 elements. Creating vector time with 772 elements. Creating vector esd_min with 772 elements. Creating vector time with 772 elements. Creating vector esd_max with 772 elements. Creating vector time with 772 elements. Creating vector esd_std with 772 elements. Creating vector time with 772 elements. Creating vector countSum with 772 elements. Creating vector time with 772 elements. Creating vector snapshot with 772 elements. Creating vector time with 772 elements. Creating vector threshold with 772 elements. Creating vector time with 772 elements. Creating vector sampleCount with 772 elements. Creating vector time with 772 elements. Creating vector flowCount with 772 elements. Creating vector time with 772 elements. Creating vector flowTime with 772 elements. Creating vector time with 772 elements. Creating vector bufferStatus with 772 elements. Creating vector time with 772 elements. Creating vector laserLevel with 772 elements. Creating vector time with 772 elements. Creating vector counter with 772 elements. Creating vector time with 772 elements. Creating vector counterPeriod with 772 elements. Creating vector time with 772 elements. Creating vector laserControl with 772 elements. Creating vector time with 772 elements. Creating vector countUnknownFrameCharacter with 772 elements. Creating vector time with 772 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 772 elements. Creating vector time with 772 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 772 elements. Creating vector time with 772 elements. Creating vector flowSpeed with 772 elements. Creating vector time with 772 elements. Creating vector countShortLFrameError with 772 elements. Creating vector time with 772 elements. Creating vector countGarbledLFrame with 772 elements. Creating vector time with 772 elements. Creating vector cFrameEsecs with 772 elements. Creating vector time with 772 elements. Creating vector correctedSampleCountList with 772 elements. Creating vector time with 772 elements. Creating vector time with 772 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014107/2014.107.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.107.00.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_2014.107.00.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_2014_107_00_107_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00.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 = 80 Gridding with nix = 240, iZ = 159 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... bbp420 bbp700 fl700_uncorr N BL BLflow LOPC count transCount nonTransCount LCcount Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 54717 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. Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118899 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 04/17/2014 05:30 to 04/17/2014 10:29 swr = 1.9235 13.7087 118.9977 137.2786 212.0506 351.6350 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_swr.png [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 564) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Done plotting SWR. Executing: /bin/rm -f ../results/2014107_GulperTimes.txt && touch ../results/2014107_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/2014/2014107/2014.107.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2014/2014107/2014.107.00/syslog -startEsecs 1397745844.6865 -surveyName Dorado389_2014_107_00_107_00 >> ../results/2014107_GulperTimes.txt Executing: removeGulpDups.py ../results/2014107_GulperTimes.txt Bottle: 0 Time: 1397746165 Depth: 17.8608 Dist: 0.27963 Bottle: 1 Time: 1397746887 Depth: 17.1042 Dist: 1.2166 Bottle: 2 Time: 1397748488 Depth: 12.2483 Dist: 3.2464 Bottle: 3 Time: 1397750185 Depth: 26.5705 Dist: 5.4733 Bottle: 4 Time: 1397750211 Depth: 19.2269 Dist: 5.5133 Bottle: 5 Time: 1397753064 Depth: 2.7744 Dist: 9.3866 Bottle: 6 Time: 1397753952 Depth: 7.8768 Dist: 10.5631 Bottle: 7 Time: 1397754793 Depth: 27.2783 Dist: 11.7279 Bottle: 8 Time: 1397755523 Depth: 16.8183 Dist: 12.6457 Bottle: 9 Time: 1397755549 Depth: 26.9666 Dist: 12.6787 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 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 2Column contouring gridded variable gT 2Column contouring gridded variable gS 2Column contouring gridded variable gN 2Column contouring gridded variable gO 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_2column.png Elapsed time to save image: 5 seconds Biolume contouring gridded variable gD Biolume contouring gridded variable gT Biolume contouring gridded variable gS Biolume contouring gridded variable gN Biolume contouring gridded variable gO Biolume contouring gridded variable gB420 Biolume contouring gridded variable gB700 Biolume contouring gridded variable gF Biolume contouring gridded variable gBL Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_biolume.png Elapsed time to save image: 24 seconds 2Column contouring gridded variable gLOPCcount 2Column contouring gridded variable gLOPCtransCount 2Column contouring gridded variable gLOPCnonTransCount 2Column contouring gridded variable gLOPCLCcount 2Column contouring gridded variable gT 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_lopc.png Elapsed time to save image: 5 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_2014_107_00_107_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_2column.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2014/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_2014_107_00_107_00_Temperature.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2014/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_2014_107_00_107_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2014/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_2014_107_00_107_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2014/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_2014_107_00_107_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2014/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2014/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2014/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.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2014/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2014_107_00_107_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00.kml... Copied to /mbari/AUVCTD/surveys/2014/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_107_00_107_00_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_2014_107_00_107_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 6 NaNs found in bbpRed. Interpolating anyway. Encountered 57 NaN values in array of lon that is 8566 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_2014_107_00_107_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00.txt... Copied to /mbari/AUVCTD/surveys/2014/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2014/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 6 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2014/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_2014_107_00_107_00.nc... Copied to /mbari/AUVCTD/surveys/2014/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2014/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_107_00_107_00.mat... Copied to /mbari/AUVCTD/surveys/2014/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2014_107_00_107_00 processed" mccann@mbari.org < mail_Dorado389_2014_107_00_107_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.107.00.mat Processing time: 82 seconds