Execution of AUVprocess_main version 1.87 at 2018-08-10T21:59:04Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2010, ['174.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.174.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/navigation.nc')
Creating vector time with 311824 elements.
Creating vector mPos_x with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mPos_y with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mDepth with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mGpsNorth with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mGpsEast with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mGpsValid with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mPhi with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mTheta with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mPsi with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mOmega_x with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mOmega_y with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mOmega_z with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mPsaRange with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mAltitude with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mDvlAltitude with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mWaterSpeed with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mDvlValid with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mDvlNewData with 311824 elements.
Creating vector time with 311824 elements.
Creating vector mDeltaT with 311824 elements.
Creating vector time with 311824 elements.
Creating vector nfix with 311824 elements.
Creating vector time with 311824 elements.
Creating vector efix with 311824 elements.
Creating vector time with 311824 elements.
Creating vector filter_north with 311824 elements.
Creating vector time with 311824 elements.
Creating vector filter_east with 311824 elements.
Creating vector time with 311824 elements.
Creating vector filter_depth with 311824 elements.
Creating vector time with 311824 elements.
Creating vector north_current with 311824 elements.
Creating vector time with 311824 elements.
Creating vector east_current with 311824 elements.
Creating vector time with 311824 elements.
Creating vector speed_bias with 311824 elements.
Creating vector time with 311824 elements.
Creating vector heading_bias with 311824 elements.
Creating vector time with 311824 elements.
Creating vector latitude with 311824 elements.
Creating vector time with 311824 elements.
Creating vector longitude with 311824 elements.
Creating vector time with 311824 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/navigation.nc');
[Warning: P-file /mbari/matlab/toolbox/matlab/strfun/num2str.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/strfun/num2str.m.
/mbari/matlab/toolbox/matlab/strfun/num2str.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In processNav (line 62)
  In processAUVmission (line 60)
  In AUVprocess_main (line 225)] 
processNav(): median of positive valued depths = 13.3887
processNav(): Finding depths less than 93.721 and times > 0
processNav(): length(Nav.depth) = 311824
processNav(): length(gindx)     = 311824
 
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/2010/2010174/2010.174.00/gps.nc')
Creating vector time with 1557 elements.
Creating vector hours with 1557 elements.
Creating vector time with 1557 elements.
Creating vector minutes with 1557 elements.
Creating vector time with 1557 elements.
Creating vector seconds with 1557 elements.
Creating vector time with 1557 elements.
Creating vector centiSeconds with 1557 elements.
Creating vector time with 1557 elements.
Creating vector latitude with 1557 elements.
Creating vector time with 1557 elements.
Creating vector longitude with 1557 elements.
Creating vector time with 1557 elements.
Creating vector quality with 1557 elements.
Creating vector time with 1557 elements.
Creating vector numberOfSatellites with 1557 elements.
Creating vector time with 1557 elements.
Creating vector hdop with 1557 elements.
Creating vector time with 1557 elements.
Creating vector antennaHeight with 1557 elements.
Creating vector time with 1557 elements.
Creating vector geoHeight with 1557 elements.
Creating vector time with 1557 elements.
Creating vector dgpsDataAge with 1557 elements.
Creating vector time with 1557 elements.
Creating vector dgpsRSID with 1557 elements.
Creating vector time with 1557 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/parosci.nc')
Creating vector time with 509475 elements.
Creating vector depth with 509475 elements.
Creating vector time with 509475 elements.
Creating vector temp with 509475 elements.
Creating vector time with 509475 elements.
Creating vector pressure with 509475 elements.
Creating vector time with 509475 elements.
Creating vector temp_period with 509475 elements.
Creating vector time with 509475 elements.
Creating vector pres_period with 509475 elements.
Creating vector time with 509475 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.47755 max(Depth.data) = 27.0989
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.47755 max(Depth.data) = 27.0989
[Warning: P-file /mbari/matlab/toolbox/matlab/ops/unique.p is older than MATLAB
file /mbari/matlab/toolbox/matlab/ops/unique.m.
/mbari/matlab/toolbox/matlab/ops/unique.p may be obsolete and may need to be
regenerated.
Type "help pcode" for information about generating P-files.] 
[> In fix_depth_time (line 6)
  In processDepth (line 65)
  In processAUVmission (line 106)
  In AUVprocess_main (line 225)] 
 
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/2010/2010174/2010.174.00/hydroscatlog.nc')
Creating vector time with 249515 elements.
Creating vector Seconds with 249515 elements.
Creating vector time with 249515 elements.
Creating vector HundrethsOfSeconds with 249515 elements.
Creating vector time with 249515 elements.
Creating vector Snorm1 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector Snorm2 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector Snorm3 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector Gain_Status_1 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector Gain_Status_2 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector Gain_Status_3 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector RawDepthValue with 249515 elements.
Creating vector time with 249515 elements.
Creating vector RawTempValue with 249515 elements.
Creating vector time with 249515 elements.
Creating vector Temperature with 249515 elements.
Creating vector time with 249515 elements.
Creating vector ErrorValue with 249515 elements.
Creating vector time with 249515 elements.
Creating vector bb470 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector bb676 with 249515 elements.
Creating vector time with 249515 elements.
Creating vector fl676u with 249515 elements.
Creating vector time with 249515 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/ctdDriver.nc')
Creating vector time with 249497 elements.
Creating vector conductivity with 249497 elements.
Creating vector time with 249497 elements.
Creating vector temperature with 249497 elements.
Creating vector time with 249497 elements.
Creating vector cond_frequency with 249497 elements.
Creating vector time with 249497 elements.
Creating vector temp_frequency with 249497 elements.
Creating vector time with 249497 elements.
Creating vector spare with 249497 elements.
Creating vector time with 249497 elements.
Creating vector humidity with 249497 elements.
Creating vector time with 249497 elements.
Creating vector flow1 with 249497 elements.
Creating vector time with 249497 elements.
Creating vector rhodamine with 249497 elements.
Creating vector time with 249497 elements.
Creating vector dissolvedO2 with 249497 elements.
Creating vector time with 249497 elements.
Creating vector salinity with 249497 elements.
Creating vector time with 249497 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/ctdDriver2.nc')
Creating vector time with 249562 elements.
Creating vector conductivity with 249562 elements.
Creating vector time with 249562 elements.
Creating vector temperature with 249562 elements.
Creating vector time with 249562 elements.
Creating vector cond_frequency with 249562 elements.
Creating vector time with 249562 elements.
Creating vector temp_frequency with 249562 elements.
Creating vector time with 249562 elements.
Creating vector flow2 with 249562 elements.
Creating vector time with 249562 elements.
Creating vector spare with 249562 elements.
Creating vector time with 249562 elements.
Creating vector salinity with 249562 elements.
Creating vector time with 249562 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/isuslog.nc')
Creating vector time with 48447 elements.
Creating vector isusNitrate with 48447 elements.
Creating vector time with 48447 elements.
Creating vector isusTemp with 48447 elements.
Creating vector time with 48447 elements.
Creating vector isusQuality with 48447 elements.
Creating vector time with 48447 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
Processing Biolume data...
[Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/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/2010/2010174/2010.174.00/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/2010/2010174/2010.174.00/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/2010/2010174/2010.174.00/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/2010/2010174/2010.174.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (1029 x 994) with 1022826 elements.
Creating vector time with 1029 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (1029 x 994) with 1022826 elements.
Creating vector time with 1029 elements.
Creating vector bin with 994 elements.
Creating matrix countList (1029 x 994) with 1022826 elements.
Creating vector time with 1029 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 1029 elements.
Creating vector time with 1029 elements.
Creating vector transCount with 1029 elements.
Creating vector time with 1029 elements.
Creating vector nonTransCount with 1029 elements.
Creating vector time with 1029 elements.
Creating vector ai_mean with 1029 elements.
Creating vector time with 1029 elements.
Creating vector ai_min with 1029 elements.
Creating vector time with 1029 elements.
Creating vector ai_max with 1029 elements.
Creating vector time with 1029 elements.
Creating vector ai_std with 1029 elements.
Creating vector time with 1029 elements.
Creating vector esd_mean with 1029 elements.
Creating vector time with 1029 elements.
Creating vector esd_min with 1029 elements.
Creating vector time with 1029 elements.
Creating vector esd_max with 1029 elements.
Creating vector time with 1029 elements.
Creating vector esd_std with 1029 elements.
Creating vector time with 1029 elements.
Creating vector countSum with 1029 elements.
Creating vector time with 1029 elements.
Creating vector snapshot with 1029 elements.
Creating vector time with 1029 elements.
Creating vector threshold with 1029 elements.
Creating vector time with 1029 elements.
Creating vector sampleCount with 1029 elements.
Creating vector time with 1029 elements.
Creating vector flowCount with 1029 elements.
Creating vector time with 1029 elements.
Creating vector flowTime with 1029 elements.
Creating vector time with 1029 elements.
Creating vector bufferStatus with 1029 elements.
Creating vector time with 1029 elements.
Creating vector laserLevel with 1029 elements.
Creating vector time with 1029 elements.
Creating vector counter with 1029 elements.
Creating vector time with 1029 elements.
Creating vector counterPeriod with 1029 elements.
Creating vector time with 1029 elements.
Creating vector laserControl with 1029 elements.
Creating vector time with 1029 elements.
Creating vector countUnknownFrameCharacter with 1029 elements.
Creating vector time with 1029 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1029 elements.
Creating vector time with 1029 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1029 elements.
Creating vector time with 1029 elements.
Creating vector flowSpeed with 1029 elements.
Creating vector time with 1029 elements.
Creating vector countShortLFrameError with 1029 elements.
Creating vector time with 1029 elements.
Creating vector countGarbledLFrame with 1029 elements.
Creating vector time with 1029 elements.
Creating vector cFrameEsecs with 1029 elements.
Creating vector time with 1029 elements.
Creating vector correctedSampleCountList with 1029 elements.
Creating vector time with 1029 elements.
Creating vector time with 1029 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010174/2010.174.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.174.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...

SecondaryDissolvedO2 =

     []

Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.174.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 29 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_nav_adjust.png
[Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imformats.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imformats.m.
/mbari/matlab/toolbox/matlab/imagesci/imformats.p may be obsolete and may need
to be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In imwrite>parse_inputs (line 557)
  In imwrite (line 418)
  In writeRaster
  In printingGenerateOutput
  In alternatePrintPath
  In print (line 82)
  In create_data_products (line 99)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
[Warning: P-file /mbari/matlab/toolbox/matlab/timefun/datevec.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/timefun/datevec.m.
/mbari/matlab/toolbox/matlab/timefun/datevec.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In datenum (line 103)
  In writepng (line 232)
  In imwrite (line 485)
  In writeRaster
  In printingGenerateOutput
  In alternatePrintPath
  In print (line 82)
  In create_data_products (line 99)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00.mat
 
 
*************************************************************************
Calling plot_sections from ../viz to produce section plots ...
Using median boxcar filter of vector...
Using mean boxcar filter of vector...
Number of profiles found = 848 Gridding with nix = 2544, iZ = 51
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
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 355)
  In create_data_products (line 120)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
     transCount
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 357)
  In create_data_products (line 120)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
     nonTransCount
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 359)
  In create_data_products (line 120)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
     LCcount
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 361)
  In create_data_products (line 120)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
 
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 311694 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 311694 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2010174_GulperTimes.txt && touch ../results/2010174_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/2010/2010174/2010.174.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010174/2010.174.00/syslog -startEsecs 1277331898.6552 -surveyName Dorado389_2010_174_00_174_00 >> ../results/2010174_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010174_GulperTimes.txt
Bottle: 0 Time: 1277390518.0495 Depth: 5.6722 Dist: 78.9926
Bottle: 1 Time: 1277390520 Depth: 6.2239 Dist: 78.9949
Bottle: 2 Time: 1277391162.0554 Depth: 5.8459 Dist: 79.8079
Bottle: 3 Time: 1277391164 Depth: 6.3521 Dist: 79.81
Bottle: 4 Time: 1277392133.6488 Depth: 5.7312 Dist: 81.0024
Bottle: 5 Time: 1277392135.8487 Depth: 6.137 Dist: 81.005
Bottle: 6 Time: 1277393173.6576 Depth: 5.6485 Dist: 82.3203
Bottle: 7 Time: 1277393175.8574 Depth: 6.1985 Dist: 82.3227
Bottle: 8 Time: 1277394180.6486 Depth: 3.8993 Dist: 83.6495
Bottle: 9 Time: 1277394182.8484 Depth: 3.3764 Dist: 83.6509
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_gridded.mat

outvarstr =

    'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth '

2Column contouring gridded variable gD
2Column contouring gridded variable gT
2Column contouring gridded variable gS
2Column contouring gridded variable gN
2Column contouring gridded variable gO
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_2column.png
Elapsed time to save image: 9 seconds
Biolume contouring gridded variable gD
Biolume contouring gridded variable gT
Biolume contouring gridded variable gS
Biolume contouring gridded variable gN
Biolume contouring gridded variable gO
Biolume contouring gridded variable gB420
Biolume contouring gridded variable gB700
Biolume contouring gridded variable gF
Biolume contouring gridded variable gBL
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_biolume.png
Elapsed time to save image: 37 seconds
2Column contouring gridded variable gLOPCcount
2Column contouring gridded variable gLOPCtransCount
2Column contouring gridded variable gLOPCnonTransCount
2Column contouring gridded variable gLOPCLCcount
2Column contouring gridded variable gT
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_lopc.png
Elapsed time to save image: 8 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
[Warning: P-file /mbari/matlab/toolbox/matlab/graph2d/subplot.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/graph2d/subplot.m.
/mbari/matlab/toolbox/matlab/graph2d/subplot.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In plot_survey_stats (line 47)
  In create_data_products (line 134)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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.
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for LOPC Total Count           
Creating Dorado389_2010_174_00_174_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00.kml...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_174_00_174_00_Bioluminescence.kml'
not found.] 
[> In create_data_products (line 420)
  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_2010_174_00_174_00.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpRed.  Interpolating anyway.
Encountered 21 NaN values in array of lon that is 48446 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 48425 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 48425 are not equal to number of Lat lon points = 48446
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_2010_174_00_174_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00.txt...
Copied to /mbari/AUVCTD/surveys/2010/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2010/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...
2 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_174_00_174_00.nc...
Copied to /mbari/AUVCTD/surveys/2010/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2010/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_174_00_174_00.mat...
Copied to /mbari/AUVCTD/surveys/2010/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2010_174_00_174_00 processed" mccann@mbari.org < mail_Dorado389_2010_174_00_174_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.174.00.mat
Processing time: 193 seconds