Execution of AUVprocess_main version 1.86 at 2018-05-25T18:47:26Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2015, ['265.03'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
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Processing data from SSDS via DODS server
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*************************************************************************
Processing AUV mission: 2015.265.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/
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/2015/2015265/2015.265.03/navigation.nc')
Creating vector time with 446703 elements.
Creating vector mPos_x with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mPos_y with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mDepth with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mGpsNorth with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mGpsEast with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mGpsValid with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mPhi with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mTheta with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mPsi with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mOmega_x with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mOmega_y with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mOmega_z with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mPsaRange with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mAltitude with 446703 elements.
Creating vector time with 446703 elements.
Creating vector multibeamAltitude with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mDvlAltitude with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mEchoAltitude with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mEchoHorizRange with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mEchoAltitudeLast with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mEchoHorizRangeLast with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mEchoNumOfPings with 446703 elements.
Creating vector time with 446703 elements.
Creating vector nadirCnts with 446703 elements.
Creating vector time with 446703 elements.
Creating vector obstacleCnts with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mWaterSpeed with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mDvlValid with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mDvlNewData with 446703 elements.
Creating vector time with 446703 elements.
Creating vector mDeltaT with 446703 elements.
Creating vector time with 446703 elements.
Creating vector nfix with 446703 elements.
Creating vector time with 446703 elements.
Creating vector efix with 446703 elements.
Creating vector time with 446703 elements.
Creating vector filter_north with 446703 elements.
Creating vector time with 446703 elements.
Creating vector filter_east with 446703 elements.
Creating vector time with 446703 elements.
Creating vector filter_depth with 446703 elements.
Creating vector time with 446703 elements.
Creating vector north_current with 446703 elements.
Creating vector time with 446703 elements.
Creating vector east_current with 446703 elements.
Creating vector time with 446703 elements.
Creating vector speed_bias with 446703 elements.
Creating vector time with 446703 elements.
Creating vector heading_bias with 446703 elements.
Creating vector time with 446703 elements.
Creating vector latitude with 446703 elements.
Creating vector time with 446703 elements.
Creating vector longitude with 446703 elements.
Creating vector time with 446703 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/navigation.nc');
processNav(): median of positive valued depths = 36.7387
processNav(): Finding depths less than 257.1707 and times > 0
processNav(): length(Nav.depth) = 446703
processNav(): length(gindx)     = 446703
 
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/2015/2015265/2015.265.03/gps.nc')
Creating vector time with 7855 elements.
Creating vector hours with 7855 elements.
Creating vector time with 7855 elements.
Creating vector minutes with 7855 elements.
Creating vector time with 7855 elements.
Creating vector seconds with 7855 elements.
Creating vector time with 7855 elements.
Creating vector centiSeconds with 7855 elements.
Creating vector time with 7855 elements.
Creating vector latitude with 7855 elements.
Creating vector time with 7855 elements.
Creating vector longitude with 7855 elements.
Creating vector time with 7855 elements.
Creating vector quality with 7855 elements.
Creating vector time with 7855 elements.
Creating vector numberOfSatellites with 7855 elements.
Creating vector time with 7855 elements.
Creating vector hdop with 7855 elements.
Creating vector time with 7855 elements.
Creating vector antennaHeight with 7855 elements.
Creating vector time with 7855 elements.
Creating vector geoHeight with 7855 elements.
Creating vector time with 7855 elements.
Creating vector dgpsDataAge with 7855 elements.
Creating vector time with 7855 elements.
Creating vector dgpsRSID with 7855 elements.
Creating vector time with 7855 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/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/2015/2015265/2015.265.03/parosci.nc')
Creating vector time with 876772 elements.
Creating vector depth with 876772 elements.
Creating vector time with 876772 elements.
Creating vector temp with 876772 elements.
Creating vector time with 876772 elements.
Creating vector pressure with 876772 elements.
Creating vector time with 876772 elements.
Creating vector temp_period with 876772 elements.
Creating vector time with 876772 elements.
Creating vector pres_period with 876772 elements.
Creating vector time with 876772 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.40538 max(Depth.data) = 77.2672
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.40538 max(Depth.data) = 77.2672
 
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/2015/2015265/2015.265.03/hydroscatlog.nc')
Creating vector time with 357338 elements.
Creating vector Seconds with 357338 elements.
Creating vector time with 357338 elements.
Creating vector HundrethsOfSeconds with 357338 elements.
Creating vector time with 357338 elements.
Creating vector Snorm1 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector Snorm2 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector Snorm3 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector Gain_Status_1 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector Gain_Status_2 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector Gain_Status_3 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector RawDepthValue with 357338 elements.
Creating vector time with 357338 elements.
Creating vector RawTempValue with 357338 elements.
Creating vector time with 357338 elements.
Creating vector Temperature with 357338 elements.
Creating vector time with 357338 elements.
Creating vector ErrorValue with 357338 elements.
Creating vector time with 357338 elements.
Creating vector bb470 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector bb676 with 357338 elements.
Creating vector time with 357338 elements.
Creating vector fl676u with 357338 elements.
Creating vector time with 357338 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/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/2015/2015265/2015.265.03/ctdDriver.nc')
Creating vector time with 357423 elements.
Creating vector conductivity with 357423 elements.
Creating vector time with 357423 elements.
Creating vector temperature with 357423 elements.
Creating vector time with 357423 elements.
Creating vector cond_frequency with 357423 elements.
Creating vector time with 357423 elements.
Creating vector temp_frequency with 357423 elements.
Creating vector time with 357423 elements.
Creating vector spare with 357423 elements.
Creating vector time with 357423 elements.
Creating vector humidity with 357423 elements.
Creating vector time with 357423 elements.
Creating vector flow1 with 357423 elements.
Creating vector time with 357423 elements.
Creating vector CDOM with 357423 elements.
Creating vector time with 357423 elements.
Creating vector dissolvedO2 with 357423 elements.
Creating vector time with 357423 elements.
Creating vector salinity with 357423 elements.
Creating vector time with 357423 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/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/2015/2015265/2015.265.03/ctdDriver2.nc')
Creating vector time with 357421 elements.
Creating vector conductivity with 357421 elements.
Creating vector time with 357421 elements.
Creating vector temperature with 357421 elements.
Creating vector time with 357421 elements.
Creating vector cond_frequency with 357421 elements.
Creating vector time with 357421 elements.
Creating vector temp_frequency with 357421 elements.
Creating vector time with 357421 elements.
Creating vector flow2 with 357421 elements.
Creating vector time with 357421 elements.
Creating vector spare with 357421 elements.
Creating vector time with 357421 elements.
Creating vector salinity with 357421 elements.
Creating vector time with 357421 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/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/2015/2015265/2015.265.03/isuslog.nc')
Creating vector time with 69431 elements.
Creating vector isusNitrate with 69431 elements.
Creating vector time with 69431 elements.
Creating vector isusTemp with 69431 elements.
Creating vector time with 69431 elements.
Creating vector isusQuality with 69431 elements.
Creating vector time with 69431 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/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 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/2015/2015265/2015.265.03/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (8509 x 994) with 8457946 elements.
Creating vector time with 8509 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (8509 x 994) with 8457946 elements.
Creating vector time with 8509 elements.
Creating vector bin with 994 elements.
Creating matrix countList (8509 x 994) with 8457946 elements.
Creating vector time with 8509 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 8509 elements.
Creating vector time with 8509 elements.
Creating vector transCount with 8509 elements.
Creating vector time with 8509 elements.
Creating vector nonTransCount with 8509 elements.
Creating vector time with 8509 elements.
Creating vector ai_mean with 8509 elements.
Creating vector time with 8509 elements.
Creating vector ai_min with 8509 elements.
Creating vector time with 8509 elements.
Creating vector ai_max with 8509 elements.
Creating vector time with 8509 elements.
Creating vector ai_std with 8509 elements.
Creating vector time with 8509 elements.
Creating vector esd_mean with 8509 elements.
Creating vector time with 8509 elements.
Creating vector esd_min with 8509 elements.
Creating vector time with 8509 elements.
Creating vector esd_max with 8509 elements.
Creating vector time with 8509 elements.
Creating vector esd_std with 8509 elements.
Creating vector time with 8509 elements.
Creating vector countSum with 8509 elements.
Creating vector time with 8509 elements.
Creating vector snapshot with 8509 elements.
Creating vector time with 8509 elements.
Creating vector threshold with 8509 elements.
Creating vector time with 8509 elements.
Creating vector sampleCount with 8509 elements.
Creating vector time with 8509 elements.
Creating vector flowCount with 8509 elements.
Creating vector time with 8509 elements.
Creating vector flowTime with 8509 elements.
Creating vector time with 8509 elements.
Creating vector bufferStatus with 8509 elements.
Creating vector time with 8509 elements.
Creating vector laserLevel with 8509 elements.
Creating vector time with 8509 elements.
Creating vector counter with 8509 elements.
Creating vector time with 8509 elements.
Creating vector counterPeriod with 8509 elements.
Creating vector time with 8509 elements.
Creating vector laserControl with 8509 elements.
Creating vector time with 8509 elements.
Creating vector countUnknownFrameCharacter with 8509 elements.
Creating vector time with 8509 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 8509 elements.
Creating vector time with 8509 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 8509 elements.
Creating vector time with 8509 elements.
Creating vector flowSpeed with 8509 elements.
Creating vector time with 8509 elements.
Creating vector countShortLFrameError with 8509 elements.
Creating vector time with 8509 elements.
Creating vector countGarbledLFrame with 8509 elements.
Creating vector time with 8509 elements.
Creating vector cFrameEsecs with 8509 elements.
Creating vector time with 8509 elements.
Creating vector correctedSampleCountList with 8509 elements.
Creating vector time with 8509 elements.
Creating vector time with 8509 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2015/2015265/2015.265.03/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015.265.03.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/src/matlab/doradosdp/results/Dorado389_2015.265.03.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 3 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_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 = 680 Gridding with nix = 2040, iZ = 152
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
Only one good point or fewer - NaNing the gBL array.
   BLflow
Only one good point or fewer - NaNing the gBLflow array.
   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
No valid data for gBL
  cvarname = gBLflow
No valid data for gBLflow
  cvarname = gLOPCcount
  cvarname = gLOPCtransCount
  cvarname = gLOPCnonTransCount
  cvarname = gLOPCLCcount
Encountered 0 NaN values in array of lon that is 341819 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 <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 341819 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2015265_GulperTimes.txt && touch ../results/2015265_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/2015/2015265/2015.265.03/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2015/2015265/2015.265.03/syslog -startEsecs 1442940152.802 -surveyName Dorado389_2015_265_03_265_03 >> ../results/2015265_GulperTimes.txt
Executing: removeGulpDups.py ../results/2015265_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_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
  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 gB420
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB700
  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/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_2column.png
Elapsed time to save image: 15 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 gB420
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB700
  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/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_biolume.png
Elapsed time to save image: 65 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 gB420
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB700
  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/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_lopc.png
Elapsed time to save image: 16 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_2015_265_03_265_03_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_2column.png...
Copied to /mbari/AUVCTD/surveys/2015/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_biolume.png...
Copied to /mbari/AUVCTD/surveys/2015/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_lopc.png...
Copied to /mbari/AUVCTD/surveys/2015/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2015/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2015/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2015/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03_LOPC_Total_Count.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2015/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2015_265_03_265_03.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03.kml...
Copied to /mbari/AUVCTD/surveys/2015/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2015_265_03_265_03_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_2015_265_03_265_03.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
5 NaNs found in bbpBlue.  Interpolating anyway.
8 NaNs found in bbpRed.  Interpolating anyway.
Encountered 16281 NaN values in array of lon that is 69431 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 <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 53150 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 53150 are not equal to number of Lat lon points = 69431
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_2015_265_03_265_03.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03.txt...
Copied to /mbari/AUVCTD/surveys/2015/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2015/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
5 NaNs found in bbpBlue.  Interpolating anyway.
8 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_decim.nc...
Copied to /mbari/AUVCTD/surveys/2015/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_2015_265_03_265_03.nc...
Copied to /mbari/AUVCTD/surveys/2015/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2015/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015_265_03_265_03.mat...
Copied to /mbari/AUVCTD/surveys/2015/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2015_265_03_265_03 processed" mccann@mbari.org < mail_Dorado389_2015_265_03_265_03.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2015.265.03.mat
Processing time: 399 seconds