Execution of AUVprocess_main version 1.88 at 2020-11-24T21:44:29Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2020, ['301.03'], '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: 2020.301.03 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/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/2020/2020301/2020.301.03/navigation.nc') Creating vector time with 369003 elements. Creating vector mPos_x with 369003 elements. Creating vector time with 369003 elements. Creating vector mPos_y with 369003 elements. Creating vector time with 369003 elements. Creating vector mDepth with 369003 elements. Creating vector time with 369003 elements. Creating vector mGpsNorth with 369003 elements. Creating vector time with 369003 elements. Creating vector mGpsEast with 369003 elements. Creating vector time with 369003 elements. Creating vector mGpsValid with 369003 elements. Creating vector time with 369003 elements. Creating vector mPhi with 369003 elements. Creating vector time with 369003 elements. Creating vector mTheta with 369003 elements. Creating vector time with 369003 elements. Creating vector mPsi with 369003 elements. Creating vector time with 369003 elements. Creating vector mOmega_x with 369003 elements. Creating vector time with 369003 elements. Creating vector mOmega_y with 369003 elements. Creating vector time with 369003 elements. Creating vector mOmega_z with 369003 elements. Creating vector time with 369003 elements. Creating vector mPsaRange with 369003 elements. Creating vector time with 369003 elements. Creating vector mAltitude with 369003 elements. Creating vector time with 369003 elements. Creating vector multibeamAltitude with 369003 elements. Creating vector time with 369003 elements. Creating vector mDvlAltitude with 369003 elements. Creating vector time with 369003 elements. Creating vector mEchoAltitude with 369003 elements. Creating vector time with 369003 elements. Creating vector mEchoHorizRange with 369003 elements. Creating vector time with 369003 elements. Creating vector mEchoAltitudeLast with 369003 elements. Creating vector time with 369003 elements. Creating vector mEchoHorizRangeLast with 369003 elements. Creating vector time with 369003 elements. Creating vector mEchoNumOfPings with 369003 elements. Creating vector time with 369003 elements. Creating vector nadirCnts with 369003 elements. Creating vector time with 369003 elements. Creating vector obstacleCnts with 369003 elements. Creating vector time with 369003 elements. Creating vector nGoodNadirBeams with 369003 elements. Creating vector time with 369003 elements. Creating vector medianNadirBeamNo with 369003 elements. Creating vector time with 369003 elements. Creating vector mWaterSpeed with 369003 elements. Creating vector time with 369003 elements. Creating vector mDvlValid with 369003 elements. Creating vector time with 369003 elements. Creating vector mDvlNewData with 369003 elements. Creating vector time with 369003 elements. Creating vector mDeltaT with 369003 elements. Creating vector time with 369003 elements. Creating vector nfix with 369003 elements. Creating vector time with 369003 elements. Creating vector efix with 369003 elements. Creating vector time with 369003 elements. Creating vector filter_north with 369003 elements. Creating vector time with 369003 elements. Creating vector filter_east with 369003 elements. Creating vector time with 369003 elements. Creating vector filter_depth with 369003 elements. Creating vector time with 369003 elements. Creating vector north_current with 369003 elements. Creating vector time with 369003 elements. Creating vector east_current with 369003 elements. Creating vector time with 369003 elements. Creating vector speed_bias with 369003 elements. Creating vector time with 369003 elements. Creating vector heading_bias with 369003 elements. Creating vector time with 369003 elements. Creating vector latitude with 369003 elements. Creating vector time with 369003 elements. Creating vector longitude with 369003 elements. Creating vector time with 369003 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/navigation.nc'); processNav(): median of positive valued depths = 34.1465 processNav(): Finding depths less than 239.0252 and times > 0 processNav(): length(Nav.depth) = 369003 processNav(): length(gindx) = 369003 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/2020/2020301/2020.301.03/gps.nc') Creating vector time with 22071 elements. Creating vector hours with 22071 elements. Creating vector time with 22071 elements. Creating vector minutes with 22071 elements. Creating vector time with 22071 elements. Creating vector seconds with 22071 elements. Creating vector time with 22071 elements. Creating vector centiSeconds with 22071 elements. Creating vector time with 22071 elements. Creating vector latitude with 22071 elements. Creating vector time with 22071 elements. Creating vector longitude with 22071 elements. Creating vector time with 22071 elements. Creating vector quality with 22071 elements. Creating vector time with 22071 elements. Creating vector numberOfSatellites with 22071 elements. Creating vector time with 22071 elements. Creating vector hdop with 22071 elements. Creating vector time with 22071 elements. Creating vector antennaHeight with 22071 elements. Creating vector time with 22071 elements. Creating vector geoHeight with 22071 elements. Creating vector time with 22071 elements. Creating vector dgpsDataAge with 22071 elements. Creating vector time with 22071 elements. Creating vector dgpsRSID with 22071 elements. Creating vector time with 22071 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/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/2020/2020301/2020.301.03/parosci.nc') Creating vector time with 734827 elements. Creating vector depth with 734827 elements. Creating vector time with 734827 elements. Creating vector temp with 734827 elements. Creating vector time with 734827 elements. Creating vector pressure with 734827 elements. Creating vector time with 734827 elements. Creating vector temp_period with 734827 elements. Creating vector time with 734827 elements. Creating vector pres_period with 734827 elements. Creating vector time with 734827 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.25833 max(Depth.data) = 202.4983 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.25833 max(Depth.data) = 202.4983 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/2020/2020301/2020.301.03/hydroscatlog.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/2020/2020301/2020.301.03/hydroscatlog.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/2020/2020301/2020.301.03/hydroscatlog.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/2020/2020301/2020.301.03/hydroscatlog.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 hs2 structure to NaNs. *** 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/2020/2020301/2020.301.03/ctdDriver.nc') Creating vector time with 295256 elements. Creating vector conductivity with 295256 elements. Creating vector time with 295256 elements. Creating vector temperature with 295256 elements. Creating vector time with 295256 elements. Creating vector cond_frequency with 295256 elements. Creating vector time with 295256 elements. Creating vector temp_frequency with 295256 elements. Creating vector time with 295256 elements. Creating vector spare with 295256 elements. Creating vector time with 295256 elements. Creating vector humidity with 295256 elements. Creating vector time with 295256 elements. Creating vector flow1 with 295256 elements. Creating vector time with 295256 elements. Creating vector CDOM with 295256 elements. Creating vector time with 295256 elements. Creating vector dissolvedO2 with 295256 elements. Creating vector time with 295256 elements. Creating vector salinity with 295256 elements. Creating vector time with 295256 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/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/2020/2020301/2020.301.03/ctdDriver2.nc') Creating vector time with 295256 elements. Creating vector conductivity with 295256 elements. Creating vector time with 295256 elements. Creating vector temperature with 295256 elements. Creating vector time with 295256 elements. Creating vector cond_frequency with 295256 elements. Creating vector time with 295256 elements. Creating vector temp_frequency with 295256 elements. Creating vector time with 295256 elements. Creating vector flow2 with 295256 elements. Creating vector time with 295256 elements. Creating vector par with 295256 elements. Creating vector time with 295256 elements. Creating vector spare with 295256 elements. Creating vector time with 295256 elements. Creating vector salinity with 295256 elements. Creating vector time with 295256 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/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/2020/2020301/2020.301.03/isuslog.nc') Creating vector time with 57341 elements. Creating vector isusNitrate with 57341 elements. Creating vector time with 57341 elements. Creating vector isusTemp with 57341 elements. Creating vector time with 57341 elements. Creating vector isusQuality with 57341 elements. Creating vector time with 57341 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/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 71) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 227)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 71) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 227)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/biolume.nc') Creating vector time with 72590 elements. Creating vector rrr with 72590 elements. Creating vector time with 72590 elements. Creating vector cal_striing with 72590 elements. Creating vector time with 72590 elements. Creating vector avg_biolume with 72590 elements. Creating vector time with 72590 elements. Creating vector pump with 72590 elements. Creating vector time with 72590 elements. Creating vector system_voltage with 72590 elements. Creating vector time with 72590 elements. Creating vector flow with 72590 elements. Creating vector time with 72590 elements. Creating vector HV with 72590 elements. Creating vector time with 72590 elements. Creating vector reserved with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_0 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_1 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_2 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_3 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_4 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_5 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_6 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_7 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_8 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_9 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_10 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_11 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_12 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_13 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_14 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_15 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_16 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_17 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_18 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_19 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_20 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_21 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_22 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_23 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_24 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_25 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_26 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_27 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_28 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_29 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_30 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_31 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_32 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_33 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_34 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_35 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_36 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_37 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_38 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_39 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_40 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_41 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_42 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_43 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_44 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_45 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_46 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_47 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_48 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_49 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_50 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_51 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_52 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_53 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_54 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_55 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_56 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_57 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_58 with 72590 elements. Creating vector time with 72590 elements. Creating vector raw_59 with 72590 elements. Creating vector time with 72590 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/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/2020/2020301/2020.301.03/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (7032 x 994) with 6989808 elements. Creating vector time with 7032 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (7032 x 994) with 6989808 elements. Creating vector time with 7032 elements. Creating vector bin with 994 elements. Creating matrix countList (7032 x 994) with 6989808 elements. Creating vector time with 7032 elements. Creating vector bin with 994 elements. Creating vector LCcount with 7032 elements. Creating vector time with 7032 elements. Creating vector transCount with 7032 elements. Creating vector time with 7032 elements. Creating vector nonTransCount with 7032 elements. Creating vector time with 7032 elements. Creating vector ai_mean with 7032 elements. Creating vector time with 7032 elements. Creating vector ai_min with 7032 elements. Creating vector time with 7032 elements. Creating vector ai_max with 7032 elements. Creating vector time with 7032 elements. Creating vector ai_std with 7032 elements. Creating vector time with 7032 elements. Creating vector esd_mean with 7032 elements. Creating vector time with 7032 elements. Creating vector esd_min with 7032 elements. Creating vector time with 7032 elements. Creating vector esd_max with 7032 elements. Creating vector time with 7032 elements. Creating vector esd_std with 7032 elements. Creating vector time with 7032 elements. Creating vector countSum with 7032 elements. Creating vector time with 7032 elements. Creating vector snapshot with 7032 elements. Creating vector time with 7032 elements. Creating vector threshold with 7032 elements. Creating vector time with 7032 elements. Creating vector sampleCount with 7032 elements. Creating vector time with 7032 elements. Creating vector flowCount with 7032 elements. Creating vector time with 7032 elements. Creating vector flowTime with 7032 elements. Creating vector time with 7032 elements. Creating vector bufferStatus with 7032 elements. Creating vector time with 7032 elements. Creating vector laserLevel with 7032 elements. Creating vector time with 7032 elements. Creating vector counter with 7032 elements. Creating vector time with 7032 elements. Creating vector counterPeriod with 7032 elements. Creating vector time with 7032 elements. Creating vector laserControl with 7032 elements. Creating vector time with 7032 elements. Creating vector countUnknownFrameCharacter with 7032 elements. Creating vector time with 7032 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7032 elements. Creating vector time with 7032 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7032 elements. Creating vector time with 7032 elements. Creating vector flowSpeed with 7032 elements. Creating vector time with 7032 elements. Creating vector countShortLFrameError with 7032 elements. Creating vector time with 7032 elements. Creating vector countGarbledLFrame with 7032 elements. Creating vector time with 7032 elements. Creating vector cFrameEsecs with 7032 elements. Creating vector time with 7032 elements. Creating vector correctedSampleCountList with 7032 elements. Creating vector time with 7032 elements. Creating vector time with 7032 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020301/2020.301.03/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.301.03.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.cvs/src/matlab/doradosdp/results/Dorado389_2020.301.03.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 34 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.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 = 308 Gridding with nix = 924, iZ = 402 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 Only one good point - NaNing the gB470 array. bbp676 Only one good point - NaNing the gB676 array. fl676_uncorr Only one good point - NaNing the gF array. 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 No valid data for gF cvarname = gB470 No valid data for gB470 cvarname = gB676 No valid data for gB676 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 347979 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 347979 points from grid Monterey25.grd (2876 x 2447) Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 140704 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/27/2020 10:29 to 10/28/2020 08:30 swr = 403.0547 532.2945 582.1923 585.4817 519.2025 382.8269 228.1837 76.0086 5.7351 3.0000 3.3518 3.4077 3.1960 2.3776 2.3521 3.0779 3.4558 3.4888 3.2963 3.7076 3.2069 12.5567 91.2493 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2020301_GulperTimes.txt && touch ../results/2020301_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/2020/2020301/2020.301.03/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2020/2020301/2020.301.03/syslog -startEsecs 1603826574.6726 -surveyName Dorado389_2020_301_03_301_03 >> ../results/2020301_GulperTimes.txt Executing: removeGulpDups.py ../results/2020301_GulperTimes.txt Bottle: 0 Time: 1603827903.8715 Depth: 149.9425 Dist: 1.0183 Bottle: 1 Time: 1603828058.6709 Depth: 99.9423 Dist: 1.1573 Bottle: 2 Time: 1603828181.4725 Depth: 59.9465 Dist: 1.2728 Bottle: 3 Time: 1603828302.4742 Depth: 19.9691 Dist: 1.3849 Bottle: 4 Time: 1603828360.2703 Depth: 4.9635 Dist: 1.4365 Bottle: 5 Time: 1603832469.8688 Depth: 2.1504 Dist: 5.6573 Bottle: 6 Time: 1603835970.069 Depth: -0.087272 Dist: 9.7413 Bottle: 7 Time: 1603839096.2648 Depth: -0.084264 Dist: 13.6284 Bottle: 8 Time: 1603842395.4688 Depth: 5.0378 Dist: 17.6317 Bottle: 9 Time: 1603846456.8706 Depth: 5.0423 Dist: 21.9646 Bottle: 10 Time: 1603849792.4721 Depth: 5.0123 Dist: 25.9757 Bottle: 11 Time: 1603853180.27 Depth: 5.0817 Dist: 30.1994 Bottle: 12 Time: 1603856594.4661 Depth: 5.0251 Dist: 34.2367 Bottle: 13 Time: 1603861848.0662 Depth: 5.1039 Dist: 39.8264 Bottle: 14 Time: 1603865650.4657 Depth: 5.0303 Dist: 44.2529 Bottle: 15 Time: 1603869709.4677 Depth: -0.078273 Dist: 48.8942 Bottle: 16 Time: 1603873408.6742 Depth: -0.088127 Dist: 52.9644 Bottle: 17 Time: 1603876811.0712 Depth: -0.069153 Dist: 56.8085 Bottle: 18 Time: 1603880111.2651 Depth: -0.037444 Dist: 60.5317 Bottle: 19 Time: 1603883823.4708 Depth: 5.0257 Dist: 64.4407 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_gridded.mat outvarstr = 'gF gT gN gS gD gO gB470 gB676 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_2column.png Elapsed time to save image: 12 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB470 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB676 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_biolume.png Elapsed time to save image: 48 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_lopc.png Elapsed time to save image: 13 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_2column.png... Copied to /mbari/AUVCTD/surveys/2020/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_biolume.png... Copied to /mbari/AUVCTD/surveys/2020/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_lopc.png... Copied to /mbari/AUVCTD/surveys/2020/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2020/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2020/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2020/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Optical_Backscatter_470_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Optical_Backscatter_470_nm.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Optical_Backscatter_676_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Optical_Backscatter_676_nm.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Chlorophyll_Fluorescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Creating Dorado389_2020_301_03_301_03.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.kml... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_301_03_301_03_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 419) In build_auv_survey (line 530) In AUVprocess_main (line 257)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpBlue, same as length of bbpBlue. Not Interpolating. 1 NaNs found in bbpRed, same as length of bbpRed. Not Interpolating. 1 NaNs found in flRed_uncorr, same as length of flRed_uncorr. Not Interpolating. Encountered 3274 NaN values in array of lon that is 57337 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 54063 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 54063 are not equal to number of Lat lon points = 57337 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.txt... Copied to /mbari/AUVCTD/surveys/2020/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2020/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpBlue, same as length of bbpBlue. Not Interpolating. 1 NaNs found in bbpRed, same as length of bbpRed. Not Interpolating. 1 NaNs found in flRed_uncorr, same as length of flRed_uncorr. Not Interpolating. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_decim.nc... Copied to /mbari/AUVCTD/surveys/2020/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.nc... Copied to /mbari/AUVCTD/surveys/2020/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03_gridded.mat... Copied to /mbari/AUVCTD/surveys/2020/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_301_03_301_03.mat... Copied to /mbari/AUVCTD/surveys/2020/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ permalink_url.sh http://dods.mbari.org/cgi-bin/nph-nc/data/auvctd/surveys/2020/netcdf/Dorado389_2020_301_03_301_03.nc ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2020_301_03_301_03 processed" mccann@mbari.org < mail_Dorado389_2020_301_03_301_03.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.301.03.mat Processing time: 245 seconds