Execution of AUVprocess_main version 1.86 at 2018-05-24T19:40:13Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['261.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2013.261.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/ 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/2013/2013261/2013.261.01/navigation.nc') Creating vector time with 71835 elements. Creating vector mPos_x with 71835 elements. Creating vector time with 71835 elements. Creating vector mPos_y with 71835 elements. Creating vector time with 71835 elements. Creating vector mDepth with 71835 elements. Creating vector time with 71835 elements. Creating vector mGpsNorth with 71835 elements. Creating vector time with 71835 elements. Creating vector mGpsEast with 71835 elements. Creating vector time with 71835 elements. Creating vector mGpsValid with 71835 elements. Creating vector time with 71835 elements. Creating vector mPhi with 71835 elements. Creating vector time with 71835 elements. Creating vector mTheta with 71835 elements. Creating vector time with 71835 elements. Creating vector mPsi with 71835 elements. Creating vector time with 71835 elements. Creating vector mOmega_x with 71835 elements. Creating vector time with 71835 elements. Creating vector mOmega_y with 71835 elements. Creating vector time with 71835 elements. Creating vector mOmega_z with 71835 elements. Creating vector time with 71835 elements. Creating vector mPsaRange with 71835 elements. Creating vector time with 71835 elements. Creating vector mAltitude with 71835 elements. Creating vector time with 71835 elements. Creating vector mDvlAltitude with 71835 elements. Creating vector time with 71835 elements. Creating vector mEchoAltitude with 71835 elements. Creating vector time with 71835 elements. Creating vector mEchoHorizRange with 71835 elements. Creating vector time with 71835 elements. Creating vector mEchoAltitudeLast with 71835 elements. Creating vector time with 71835 elements. Creating vector mEchoHorizRangeLast with 71835 elements. Creating vector time with 71835 elements. Creating vector mEchoNumOfPings with 71835 elements. Creating vector time with 71835 elements. Creating vector mWaterSpeed with 71835 elements. Creating vector time with 71835 elements. Creating vector mDvlValid with 71835 elements. Creating vector time with 71835 elements. Creating vector mDvlNewData with 71835 elements. Creating vector time with 71835 elements. Creating vector mDeltaT with 71835 elements. Creating vector time with 71835 elements. Creating vector nfix with 71835 elements. Creating vector time with 71835 elements. Creating vector efix with 71835 elements. Creating vector time with 71835 elements. Creating vector filter_north with 71835 elements. Creating vector time with 71835 elements. Creating vector filter_east with 71835 elements. Creating vector time with 71835 elements. Creating vector filter_depth with 71835 elements. Creating vector time with 71835 elements. Creating vector north_current with 71835 elements. Creating vector time with 71835 elements. Creating vector east_current with 71835 elements. Creating vector time with 71835 elements. Creating vector speed_bias with 71835 elements. Creating vector time with 71835 elements. Creating vector heading_bias with 71835 elements. Creating vector time with 71835 elements. Creating vector latitude with 71835 elements. Creating vector time with 71835 elements. Creating vector longitude with 71835 elements. Creating vector time with 71835 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/navigation.nc'); processNav(): median of positive valued depths = 23.5237 processNav(): Finding depths less than 164.6661 and times > 0 processNav(): length(Nav.depth) = 71835 processNav(): length(gindx) = 71835 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/2013/2013261/2013.261.01/gps.nc') Creating vector time with 511 elements. Creating vector hours with 511 elements. Creating vector time with 511 elements. Creating vector minutes with 511 elements. Creating vector time with 511 elements. Creating vector seconds with 511 elements. Creating vector time with 511 elements. Creating vector centiSeconds with 511 elements. Creating vector time with 511 elements. Creating vector latitude with 511 elements. Creating vector time with 511 elements. Creating vector longitude with 511 elements. Creating vector time with 511 elements. Creating vector quality with 511 elements. Creating vector time with 511 elements. Creating vector numberOfSatellites with 511 elements. Creating vector time with 511 elements. Creating vector hdop with 511 elements. Creating vector time with 511 elements. Creating vector antennaHeight with 511 elements. Creating vector time with 511 elements. Creating vector geoHeight with 511 elements. Creating vector time with 511 elements. Creating vector dgpsDataAge with 511 elements. Creating vector time with 511 elements. Creating vector dgpsRSID with 511 elements. Creating vector time with 511 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/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/2013/2013261/2013.261.01/parosci.nc') Creating vector time with 141352 elements. Creating vector depth with 141352 elements. Creating vector time with 141352 elements. Creating vector temp with 141352 elements. Creating vector time with 141352 elements. Creating vector pressure with 141352 elements. Creating vector time with 141352 elements. Creating vector temp_period with 141352 elements. Creating vector time with 141352 elements. Creating vector pres_period with 141352 elements. Creating vector time with 141352 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.33558 max(Depth.data) = 51.4447 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.33558 max(Depth.data) = 51.4447 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/2013/2013261/2013.261.01/hydroscatlog.nc') Creating vector time with 57537 elements. Creating vector Seconds with 57537 elements. Creating vector time with 57537 elements. Creating vector HundrethsOfSeconds with 57537 elements. Creating vector time with 57537 elements. Creating vector Snorm1 with 57537 elements. Creating vector time with 57537 elements. Creating vector Snorm2 with 57537 elements. Creating vector time with 57537 elements. Creating vector Snorm3 with 57537 elements. Creating vector time with 57537 elements. Creating vector Gain_Status_1 with 57537 elements. Creating vector time with 57537 elements. Creating vector Gain_Status_2 with 57537 elements. Creating vector time with 57537 elements. Creating vector Gain_Status_3 with 57537 elements. Creating vector time with 57537 elements. Creating vector RawDepthValue with 57537 elements. Creating vector time with 57537 elements. Creating vector RawTempValue with 57537 elements. Creating vector time with 57537 elements. Creating vector Temperature with 57537 elements. Creating vector time with 57537 elements. Creating vector ErrorValue with 57537 elements. Creating vector time with 57537 elements. Creating vector bb470 with 57537 elements. Creating vector time with 57537 elements. Creating vector bb676 with 57537 elements. Creating vector time with 57537 elements. Creating vector fl676u with 57537 elements. Creating vector time with 57537 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/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/2013/2013261/2013.261.01/ctdDriver.nc') Creating vector time with 57496 elements. Creating vector conductivity with 57496 elements. Creating vector time with 57496 elements. Creating vector temperature with 57496 elements. Creating vector time with 57496 elements. Creating vector cond_frequency with 57496 elements. Creating vector time with 57496 elements. Creating vector temp_frequency with 57496 elements. Creating vector time with 57496 elements. Creating vector spare with 57496 elements. Creating vector time with 57496 elements. Creating vector humidity with 57496 elements. Creating vector time with 57496 elements. Creating vector flow1 with 57496 elements. Creating vector time with 57496 elements. Creating vector CDOM with 57496 elements. Creating vector time with 57496 elements. Creating vector dissolvedO2 with 57496 elements. Creating vector time with 57496 elements. Creating vector salinity with 57496 elements. Creating vector time with 57496 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/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/2013/2013261/2013.261.01/ctdDriver2.nc') Creating vector time with 57495 elements. Creating vector conductivity with 57495 elements. Creating vector time with 57495 elements. Creating vector temperature with 57495 elements. Creating vector time with 57495 elements. Creating vector cond_frequency with 57495 elements. Creating vector time with 57495 elements. Creating vector temp_frequency with 57495 elements. Creating vector time with 57495 elements. Creating vector flow2 with 57495 elements. Creating vector time with 57495 elements. Creating vector spare with 57495 elements. Creating vector time with 57495 elements. Creating vector salinity with 57495 elements. Creating vector time with 57495 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/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/2013/2013261/2013.261.01/isuslog.nc') Creating vector time with 13427 elements. Creating vector isusNitrate with 13427 elements. Creating vector time with 13427 elements. Creating vector isusTemp with 13427 elements. Creating vector time with 13427 elements. Creating vector isusQuality with 13427 elements. Creating vector time with 13427 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/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/2013/2013261/2013.261.01/biolume.nc') Creating vector time with 14160 elements. Creating vector rrr with 14160 elements. Creating vector time with 14160 elements. Creating vector cal_striing with 14160 elements. Creating vector time with 14160 elements. Creating vector avg_biolume with 14160 elements. Creating vector time with 14160 elements. Creating vector pump with 14160 elements. Creating vector time with 14160 elements. Creating vector system_voltage with 14160 elements. Creating vector time with 14160 elements. Creating vector flow with 14160 elements. Creating vector time with 14160 elements. Creating vector HV with 14160 elements. Creating vector time with 14160 elements. Creating vector reserved with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_0 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_1 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_2 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_3 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_4 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_5 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_6 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_7 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_8 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_9 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_10 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_11 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_12 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_13 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_14 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_15 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_16 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_17 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_18 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_19 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_20 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_21 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_22 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_23 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_24 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_25 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_26 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_27 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_28 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_29 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_30 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_31 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_32 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_33 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_34 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_35 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_36 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_37 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_38 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_39 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_40 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_41 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_42 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_43 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_44 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_45 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_46 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_47 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_48 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_49 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_50 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_51 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_52 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_53 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_54 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_55 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_56 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_57 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_58 with 14160 elements. Creating vector time with 14160 elements. Creating vector raw_59 with 14160 elements. Creating vector time with 14160 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/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/2013/2013261/2013.261.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (1327 x 994) with 1319038 elements. Creating vector time with 1327 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (1327 x 994) with 1319038 elements. Creating vector time with 1327 elements. Creating vector bin with 994 elements. Creating matrix countList (1327 x 994) with 1319038 elements. Creating vector time with 1327 elements. Creating vector bin with 994 elements. Creating vector LCcount with 1327 elements. Creating vector time with 1327 elements. Creating vector transCount with 1327 elements. Creating vector time with 1327 elements. Creating vector nonTransCount with 1327 elements. Creating vector time with 1327 elements. Creating vector ai_mean with 1327 elements. Creating vector time with 1327 elements. Creating vector ai_min with 1327 elements. Creating vector time with 1327 elements. Creating vector ai_max with 1327 elements. Creating vector time with 1327 elements. Creating vector ai_std with 1327 elements. Creating vector time with 1327 elements. Creating vector esd_mean with 1327 elements. Creating vector time with 1327 elements. Creating vector esd_min with 1327 elements. Creating vector time with 1327 elements. Creating vector esd_max with 1327 elements. Creating vector time with 1327 elements. Creating vector esd_std with 1327 elements. Creating vector time with 1327 elements. Creating vector countSum with 1327 elements. Creating vector time with 1327 elements. Creating vector snapshot with 1327 elements. Creating vector time with 1327 elements. Creating vector threshold with 1327 elements. Creating vector time with 1327 elements. Creating vector sampleCount with 1327 elements. Creating vector time with 1327 elements. Creating vector flowCount with 1327 elements. Creating vector time with 1327 elements. Creating vector flowTime with 1327 elements. Creating vector time with 1327 elements. Creating vector bufferStatus with 1327 elements. Creating vector time with 1327 elements. Creating vector laserLevel with 1327 elements. Creating vector time with 1327 elements. Creating vector counter with 1327 elements. Creating vector time with 1327 elements. Creating vector counterPeriod with 1327 elements. Creating vector time with 1327 elements. Creating vector laserControl with 1327 elements. Creating vector time with 1327 elements. Creating vector countUnknownFrameCharacter with 1327 elements. Creating vector time with 1327 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1327 elements. Creating vector time with 1327 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1327 elements. Creating vector time with 1327 elements. Creating vector flowSpeed with 1327 elements. Creating vector time with 1327 elements. Creating vector countShortLFrameError with 1327 elements. Creating vector time with 1327 elements. Creating vector countGarbledLFrame with 1327 elements. Creating vector time with 1327 elements. Creating vector cFrameEsecs with 1327 elements. Creating vector time with 1327 elements. Creating vector correctedSampleCountList with 1327 elements. Creating vector time with 1327 elements. Creating vector time with 1327 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013261/2013.261.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.261.01.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_2013.261.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 5 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_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 = 118 Gridding with nix = 354, iZ = 100 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 71763 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 71763 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 118897 elements. *** Could not find start or end index in Met data read from http://elvis.shore.mbari.org/thredds/dodsC/agg/OS_MBARI-M1_R_M Looking for start days = 23271.7817 since 1/1/1950 Looking for end days = 23271.948 sIndx = 77896 eIndx = Met data goes from 20017.6042 to 24980.7708 No SWR data loaded from URL. Executing: /bin/rm -f ../results/2013261_GulperTimes.txt && touch ../results/2013261_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/2013/2013261/2013.261.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013261/2013.261.01/syslog -startEsecs 1379529941.8828 -surveyName Dorado389_2013_261_01_261_01 >> ../results/2013261_GulperTimes.txt Executing: removeGulpDups.py ../results/2013261_GulperTimes.txt Bottle: 0 Time: 1379530206 Depth: 19.0586 Dist: 0.32184 Bottle: 1 Time: 1379531433 Depth: 13.5703 Dist: 2.6226 Bottle: 2 Time: 1379534997 Depth: 15.8052 Dist: 8.7913 Bottle: 3 Time: 1379536529 Depth: 8.6369 Dist: 11.1629 Bottle: 4 Time: 1379538167 Depth: 13.4164 Dist: 13.8017 Bottle: 5 Time: 1379538199 Depth: 29.0013 Dist: 13.8522 Bottle: 6 Time: 1379539820 Depth: 14.2117 Dist: 16.312 Bottle: 7 Time: 1379541736 Depth: 9.4451 Dist: 19.1967 Bottle: 8 Time: 1379543728 Depth: 5.5957 Dist: 22.1528 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_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 Did not add swr plot to the image. Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_2column.png Elapsed time to save image: 6 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 SWR image not added to the plot. Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_biolume.png Elapsed time to save image: 27 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 Did not add swr plot to the image. Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_lopc.png Elapsed time to save image: 6 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_2013_261_01_261_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_2column.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Temperature.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Nitrate.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Optical_Backscatter_420_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Optical_Backscatter_700_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_Bioluminescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01_LOPC_Total_Count.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2013_261_01_261_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01.kml... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_261_01_261_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_2013_261_01_261_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 3 NaNs found in bbpBlue. Interpolating anyway. 2 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 13 NaN values in array of lon that is 13109 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 13096 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 13096 are not equal to number of Lat lon points = 13109 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2013/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... 3 NaNs found in bbpBlue. Interpolating anyway. 2 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2013/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_2013_261_01_261_01.nc... Copied to /mbari/AUVCTD/surveys/2013/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_261_01_261_01.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2013_261_01_261_01 processed" mccann@mbari.org < mail_Dorado389_2013_261_01_261_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.261.01.mat Processing time: 101 seconds