Execution of AUVprocess_main version 1.86 at 2018-05-24T22:03:17Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2014, ['210.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2014.210.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/ 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/2014/2014210/2014.210.01/navigation.nc') Creating vector time with 43244 elements. Creating vector mPos_x with 43244 elements. Creating vector time with 43244 elements. Creating vector mPos_y with 43244 elements. Creating vector time with 43244 elements. Creating vector mDepth with 43244 elements. Creating vector time with 43244 elements. Creating vector mGpsNorth with 43244 elements. Creating vector time with 43244 elements. Creating vector mGpsEast with 43244 elements. Creating vector time with 43244 elements. Creating vector mGpsValid with 43244 elements. Creating vector time with 43244 elements. Creating vector mPhi with 43244 elements. Creating vector time with 43244 elements. Creating vector mTheta with 43244 elements. Creating vector time with 43244 elements. Creating vector mPsi with 43244 elements. Creating vector time with 43244 elements. Creating vector mOmega_x with 43244 elements. Creating vector time with 43244 elements. Creating vector mOmega_y with 43244 elements. Creating vector time with 43244 elements. Creating vector mOmega_z with 43244 elements. Creating vector time with 43244 elements. Creating vector mPsaRange with 43244 elements. Creating vector time with 43244 elements. Creating vector mAltitude with 43244 elements. Creating vector time with 43244 elements. Creating vector multibeamAltitude with 43244 elements. Creating vector time with 43244 elements. Creating vector mDvlAltitude with 43244 elements. Creating vector time with 43244 elements. Creating vector mEchoAltitude with 43244 elements. Creating vector time with 43244 elements. Creating vector mEchoHorizRange with 43244 elements. Creating vector time with 43244 elements. Creating vector mEchoAltitudeLast with 43244 elements. Creating vector time with 43244 elements. Creating vector mEchoHorizRangeLast with 43244 elements. Creating vector time with 43244 elements. Creating vector mEchoNumOfPings with 43244 elements. Creating vector time with 43244 elements. Creating vector nadirCnts with 43244 elements. Creating vector time with 43244 elements. Creating vector obstacleCnts with 43244 elements. Creating vector time with 43244 elements. Creating vector mWaterSpeed with 43244 elements. Creating vector time with 43244 elements. Creating vector mDvlValid with 43244 elements. Creating vector time with 43244 elements. Creating vector mDvlNewData with 43244 elements. Creating vector time with 43244 elements. Creating vector mDeltaT with 43244 elements. Creating vector time with 43244 elements. Creating vector nfix with 43244 elements. Creating vector time with 43244 elements. Creating vector efix with 43244 elements. Creating vector time with 43244 elements. Creating vector filter_north with 43244 elements. Creating vector time with 43244 elements. Creating vector filter_east with 43244 elements. Creating vector time with 43244 elements. Creating vector filter_depth with 43244 elements. Creating vector time with 43244 elements. Creating vector north_current with 43244 elements. Creating vector time with 43244 elements. Creating vector east_current with 43244 elements. Creating vector time with 43244 elements. Creating vector speed_bias with 43244 elements. Creating vector time with 43244 elements. Creating vector heading_bias with 43244 elements. Creating vector time with 43244 elements. Creating vector latitude with 43244 elements. Creating vector time with 43244 elements. Creating vector longitude with 43244 elements. Creating vector time with 43244 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/navigation.nc'); processNav(): median of positive valued depths = 14.043 processNav(): Finding depths less than 98.3013 and times > 0 processNav(): length(Nav.depth) = 43244 processNav(): length(gindx) = 43244 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/2014/2014210/2014.210.01/gps.nc') Creating vector time with 558 elements. Creating vector hours with 558 elements. Creating vector time with 558 elements. Creating vector minutes with 558 elements. Creating vector time with 558 elements. Creating vector seconds with 558 elements. Creating vector time with 558 elements. Creating vector centiSeconds with 558 elements. Creating vector time with 558 elements. Creating vector latitude with 558 elements. Creating vector time with 558 elements. Creating vector longitude with 558 elements. Creating vector time with 558 elements. Creating vector quality with 558 elements. Creating vector time with 558 elements. Creating vector numberOfSatellites with 558 elements. Creating vector time with 558 elements. Creating vector hdop with 558 elements. Creating vector time with 558 elements. Creating vector antennaHeight with 558 elements. Creating vector time with 558 elements. Creating vector geoHeight with 558 elements. Creating vector time with 558 elements. Creating vector dgpsDataAge with 558 elements. Creating vector time with 558 elements. Creating vector dgpsRSID with 558 elements. Creating vector time with 558 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/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/2014/2014210/2014.210.01/parosci.nc') Creating vector time with 85474 elements. Creating vector depth with 85474 elements. Creating vector time with 85474 elements. Creating vector temp with 85474 elements. Creating vector time with 85474 elements. Creating vector pressure with 85474 elements. Creating vector time with 85474 elements. Creating vector temp_period with 85474 elements. Creating vector time with 85474 elements. Creating vector pres_period with 85474 elements. Creating vector time with 85474 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.15477 max(Depth.data) = 50.5568 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.15477 max(Depth.data) = 50.5568 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/2014/2014210/2014.210.01/hydroscatlog.nc') Creating vector time with 34753 elements. Creating vector Seconds with 34753 elements. Creating vector time with 34753 elements. Creating vector HundrethsOfSeconds with 34753 elements. Creating vector time with 34753 elements. Creating vector Snorm1 with 34753 elements. Creating vector time with 34753 elements. Creating vector Snorm2 with 34753 elements. Creating vector time with 34753 elements. Creating vector Snorm3 with 34753 elements. Creating vector time with 34753 elements. Creating vector Gain_Status_1 with 34753 elements. Creating vector time with 34753 elements. Creating vector Gain_Status_2 with 34753 elements. Creating vector time with 34753 elements. Creating vector Gain_Status_3 with 34753 elements. Creating vector time with 34753 elements. Creating vector RawDepthValue with 34753 elements. Creating vector time with 34753 elements. Creating vector RawTempValue with 34753 elements. Creating vector time with 34753 elements. Creating vector Temperature with 34753 elements. Creating vector time with 34753 elements. Creating vector ErrorValue with 34753 elements. Creating vector time with 34753 elements. Creating vector bb470 with 34753 elements. Creating vector time with 34753 elements. Creating vector bb676 with 34753 elements. Creating vector time with 34753 elements. Creating vector fl676u with 34753 elements. Creating vector time with 34753 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/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/2014/2014210/2014.210.01/ctdDriver.nc') Creating vector time with 34679 elements. Creating vector conductivity with 34679 elements. Creating vector time with 34679 elements. Creating vector temperature with 34679 elements. Creating vector time with 34679 elements. Creating vector cond_frequency with 34679 elements. Creating vector time with 34679 elements. Creating vector temp_frequency with 34679 elements. Creating vector time with 34679 elements. Creating vector spare with 34679 elements. Creating vector time with 34679 elements. Creating vector humidity with 34679 elements. Creating vector time with 34679 elements. Creating vector flow1 with 34679 elements. Creating vector time with 34679 elements. Creating vector CDOM with 34679 elements. Creating vector time with 34679 elements. Creating vector dissolvedO2 with 34679 elements. Creating vector time with 34679 elements. Creating vector salinity with 34679 elements. Creating vector time with 34679 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/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/2014/2014210/2014.210.01/ctdDriver2.nc') Creating vector time with 34679 elements. Creating vector conductivity with 34679 elements. Creating vector time with 34679 elements. Creating vector temperature with 34679 elements. Creating vector time with 34679 elements. Creating vector cond_frequency with 34679 elements. Creating vector time with 34679 elements. Creating vector temp_frequency with 34679 elements. Creating vector time with 34679 elements. Creating vector flow2 with 34679 elements. Creating vector time with 34679 elements. Creating vector spare with 34679 elements. Creating vector time with 34679 elements. Creating vector salinity with 34679 elements. Creating vector time with 34679 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/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/2014/2014210/2014.210.01/isuslog.nc') Creating vector time with 6715 elements. Creating vector isusNitrate with 6715 elements. Creating vector time with 6715 elements. Creating vector isusTemp with 6715 elements. Creating vector time with 6715 elements. Creating vector isusQuality with 6715 elements. Creating vector time with 6715 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/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)] [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/2014/2014210/2014.210.01/biolume.nc') Creating vector time with 8558 elements. Creating vector rrr with 8558 elements. Creating vector time with 8558 elements. Creating vector cal_striing with 8558 elements. Creating vector time with 8558 elements. Creating vector avg_biolume with 8558 elements. Creating vector time with 8558 elements. Creating vector pump with 8558 elements. Creating vector time with 8558 elements. Creating vector system_voltage with 8558 elements. Creating vector time with 8558 elements. Creating vector flow with 8558 elements. Creating vector time with 8558 elements. Creating vector HV with 8558 elements. Creating vector time with 8558 elements. Creating vector reserved with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_0 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_1 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_2 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_3 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_4 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_5 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_6 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_7 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_8 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_9 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_10 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_11 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_12 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_13 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_14 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_15 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_16 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_17 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_18 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_19 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_20 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_21 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_22 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_23 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_24 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_25 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_26 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_27 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_28 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_29 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_30 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_31 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_32 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_33 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_34 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_35 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_36 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_37 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_38 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_39 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_40 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_41 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_42 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_43 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_44 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_45 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_46 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_47 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_48 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_49 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_50 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_51 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_52 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_53 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_54 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_55 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_56 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_57 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_58 with 8558 elements. Creating vector time with 8558 elements. Creating vector raw_59 with 8558 elements. Creating vector time with 8558 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/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/2014/2014210/2014.210.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (777 x 994) with 772338 elements. Creating vector time with 777 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (777 x 994) with 772338 elements. Creating vector time with 777 elements. Creating vector bin with 994 elements. Creating matrix countList (777 x 994) with 772338 elements. Creating vector time with 777 elements. Creating vector bin with 994 elements. Creating vector LCcount with 777 elements. Creating vector time with 777 elements. Creating vector transCount with 777 elements. Creating vector time with 777 elements. Creating vector nonTransCount with 777 elements. Creating vector time with 777 elements. Creating vector ai_mean with 777 elements. Creating vector time with 777 elements. Creating vector ai_min with 777 elements. Creating vector time with 777 elements. Creating vector ai_max with 777 elements. Creating vector time with 777 elements. Creating vector ai_std with 777 elements. Creating vector time with 777 elements. Creating vector esd_mean with 777 elements. Creating vector time with 777 elements. Creating vector esd_min with 777 elements. Creating vector time with 777 elements. Creating vector esd_max with 777 elements. Creating vector time with 777 elements. Creating vector esd_std with 777 elements. Creating vector time with 777 elements. Creating vector countSum with 777 elements. Creating vector time with 777 elements. Creating vector snapshot with 777 elements. Creating vector time with 777 elements. Creating vector threshold with 777 elements. Creating vector time with 777 elements. Creating vector sampleCount with 777 elements. Creating vector time with 777 elements. Creating vector flowCount with 777 elements. Creating vector time with 777 elements. Creating vector flowTime with 777 elements. Creating vector time with 777 elements. Creating vector bufferStatus with 777 elements. Creating vector time with 777 elements. Creating vector laserLevel with 777 elements. Creating vector time with 777 elements. Creating vector counter with 777 elements. Creating vector time with 777 elements. Creating vector counterPeriod with 777 elements. Creating vector time with 777 elements. Creating vector laserControl with 777 elements. Creating vector time with 777 elements. Creating vector countUnknownFrameCharacter with 777 elements. Creating vector time with 777 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 777 elements. Creating vector time with 777 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 777 elements. Creating vector time with 777 elements. Creating vector flowSpeed with 777 elements. Creating vector time with 777 elements. Creating vector countShortLFrameError with 777 elements. Creating vector time with 777 elements. Creating vector countGarbledLFrame with 777 elements. Creating vector time with 777 elements. Creating vector cFrameEsecs with 777 elements. Creating vector time with 777 elements. Creating vector correctedSampleCountList with 777 elements. Creating vector time with 777 elements. Creating vector time with 777 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014210/2014.210.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.210.01.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_2014.210.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 4 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_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 = 96 Gridding with nix = 288, iZ = 98 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 40604 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: 07/29/2014 05:30 to 07/29/2014 10:29 swr = NaN NaN NaN NaN NaN NaN Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01_swr.png [Warning: Contour not rendered for non-finite 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/2014210_GulperTimes.txt && touch ../results/2014210_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/2014/2014210/2014.210.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2014/2014210/2014.210.01/syslog -startEsecs 1406644939.6707 -surveyName Dorado389_2014_210_01_210_01 >> ../results/2014210_GulperTimes.txt Executing: removeGulpDups.py ../results/2014210_GulperTimes.txt Bottle: 0 Time: 1406646054 Depth: 10.2663 Dist: 1.1728 Bottle: 1 Time: 1406646515 Depth: 3.3142 Dist: 1.7065 Bottle: 2 Time: 1406646869 Depth: 22.6269 Dist: 2.1187 Bottle: 3 Time: 1406647335 Depth: 4.2574 Dist: 2.6798 Bottle: 4 Time: 1406647842 Depth: 9.4253 Dist: 3.2559 Bottle: 5 Time: 1406650859 Depth: 43.1089 Dist: 6.9281 Bottle: 6 Time: 1406651253 Depth: 3.1116 Dist: 7.3868 Bottle: 7 Time: 1406651648 Depth: 3.1156 Dist: 7.8019 Bottle: 8 Time: 1406651886 Depth: 2.2806 Dist: 8.0576 Bottle: 9 Time: 1406652348 Depth: 3.2606 Dist: 8.5098 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01_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_210_01_210_01_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_210_01_210_01_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_210_01_210_01_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_210_01_210_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01_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_210_01_210_01_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_210_01_210_01_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_210_01_210_01_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_210_01_210_01_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_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_210_01_210_01_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_210_01_210_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01.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_210_01_210_01_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_210_01_210_01.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 15 NaNs found in bbpBlue. Interpolating anyway. 40 NaNs found in bbpRed. Interpolating anyway. Encountered 413 NaN values in array of lon that is 6714 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_210_01_210_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_210_01_210_01.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_210_01_210_01_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 ctd2 temperature... Interpolating ctd2 salinity... 15 NaNs found in bbpBlue. Interpolating anyway. 40 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_210_01_210_01_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_210_01_210_01.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_210_01_210_01_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_210_01_210_01.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_210_01_210_01 processed" mccann@mbari.org < mail_Dorado389_2014_210_01_210_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.210.01.mat Processing time: 69 seconds