Execution of AUVprocess_main version 1.86 at 2018-06-01T19:51:41Z on elvis
Matlab command executed: 
   AUVprocess_main('BIOLUME', 2004, ['211.01'], '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: 2004.211.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/
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/2004/2004211/2004.211.01/navigation.nc')
Creating vector time with 127539 elements.
Creating vector mPos_x with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mPos_y with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mDepth with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mGpsNorth with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mGpsEast with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mGpsValid with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mPhi with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mTheta with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mPsi with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mOmega_x with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mOmega_y with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mOmega_z with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mPsaRange with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mAltitude with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mWaterSpeed with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mDvlValid with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mDvlNewData with 127539 elements.
Creating vector time with 127539 elements.
Creating vector mDeltaT with 127539 elements.
Creating vector time with 127539 elements.
Creating vector latitude with 127539 elements.
Creating vector time with 127539 elements.
Creating vector longitude with 127539 elements.
Creating vector time with 127539 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/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 = 41.8404
processNav(): Finding depths less than 292.8825 and times > 0
processNav(): length(Nav.depth) = 127539
processNav(): length(gindx)     = 127539
 
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/2004/2004211/2004.211.01/gps.nc')
Creating vector time with 925 elements.
Creating vector hours with 925 elements.
Creating vector time with 925 elements.
Creating vector minutes with 925 elements.
Creating vector time with 925 elements.
Creating vector seconds with 925 elements.
Creating vector time with 925 elements.
Creating vector centiSeconds with 925 elements.
Creating vector time with 925 elements.
Creating vector latitude with 925 elements.
Creating vector time with 925 elements.
Creating vector longitude with 925 elements.
Creating vector time with 925 elements.
Creating vector quality with 925 elements.
Creating vector time with 925 elements.
Creating vector numberOfSatellites with 925 elements.
Creating vector time with 925 elements.
Creating vector hdop with 925 elements.
Creating vector time with 925 elements.
Creating vector antennaHeight with 925 elements.
Creating vector time with 925 elements.
Creating vector geoHeight with 925 elements.
Creating vector time with 925 elements.
Creating vector dgpsDataAge with 925 elements.
Creating vector time with 925 elements.
Creating vector dgpsRSID with 925 elements.
Creating vector time with 925 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/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/2004/2004211/2004.211.01/parosci.nc')
Creating vector time with 127638 elements.
Creating vector depth with 127638 elements.
Creating vector time with 127638 elements.
Creating vector temp with 127638 elements.
Creating vector time with 127638 elements.
Creating vector pressure with 127638 elements.
Creating vector time with 127638 elements.
Creating vector temp_period with 127638 elements.
Creating vector time with 127638 elements.
Creating vector pres_period with 127638 elements.
Creating vector time with 127638 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.31492 max(Depth.data) = 100.9862
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.31492 max(Depth.data) = 100.9862
[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/2004/2004211/2004.211.01/hydroscatlog.nc')
Creating vector time with 102042 elements.
Creating vector Seconds with 102042 elements.
Creating vector time with 102042 elements.
Creating vector HundrethsOfSeconds with 102042 elements.
Creating vector time with 102042 elements.
Creating vector Snorm1 with 102042 elements.
Creating vector time with 102042 elements.
Creating vector Snorm2 with 102042 elements.
Creating vector time with 102042 elements.
Creating vector Snorm3 with 102042 elements.
Creating vector time with 102042 elements.
Creating vector Gain_Status_1 with 102042 elements.
Creating vector time with 102042 elements.
Creating vector Gain_Status_2 with 102042 elements.
Creating vector time with 102042 elements.
Creating vector Gain_Status_3 with 102042 elements.
Creating vector time with 102042 elements.
Creating vector RawDepthValue with 102042 elements.
Creating vector time with 102042 elements.
Creating vector RawTempValue with 102042 elements.
Creating vector time with 102042 elements.
Creating vector Temperature with 102042 elements.
Creating vector time with 102042 elements.
Creating vector ErrorValue with 102042 elements.
Creating vector time with 102042 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/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/2004/2004211/2004.211.01/ctdDriver.nc')
Creating vector time with 102033 elements.
Creating vector conductivity with 102033 elements.
Creating vector time with 102033 elements.
Creating vector temperature with 102033 elements.
Creating vector time with 102033 elements.
Creating vector cond_frequency with 102033 elements.
Creating vector time with 102033 elements.
Creating vector temp_frequency with 102033 elements.
Creating vector time with 102033 elements.
Creating vector spare with 102033 elements.
Creating vector time with 102033 elements.
Creating vector humidity with 102033 elements.
Creating vector time with 102033 elements.
Creating vector flow1 with 102033 elements.
Creating vector time with 102033 elements.
Creating vector OBS with 102033 elements.
Creating vector time with 102033 elements.
Creating vector dissolvedO2 with 102033 elements.
Creating vector time with 102033 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/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/2004/2004211/2004.211.01/ctdDriver2.nc')
Creating vector time with 102034 elements.
Creating vector conductivity with 102034 elements.
Creating vector time with 102034 elements.
Creating vector temperature with 102034 elements.
Creating vector time with 102034 elements.
Creating vector cond_frequency with 102034 elements.
Creating vector time with 102034 elements.
Creating vector temp_frequency with 102034 elements.
Creating vector time with 102034 elements.
Creating vector flow2 with 102034 elements.
Creating vector time with 102034 elements.
Creating vector spare with 102034 elements.
Creating vector time with 102034 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/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/2004/2004211/2004.211.01/isuslog.nc')
Creating vector time with 15427 elements.
Creating vector isusNitrate with 15427 elements.
Creating vector time with 15427 elements.
Creating vector isusTemp with 15427 elements.
Creating vector time with 15427 elements.
Creating vector isusQuality with 15427 elements.
Creating vector time with 15427 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/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/2004/2004211/2004.211.01/biolume.nc')
Creating vector time with 25531 elements.
Creating vector rrr with 25531 elements.
Creating vector time with 25531 elements.
Creating vector cal_striing with 25531 elements.
Creating vector time with 25531 elements.
Creating vector pump with 25531 elements.
Creating vector time with 25531 elements.
Creating vector flow with 25531 elements.
Creating vector time with 25531 elements.
Creating vector humidity with 25531 elements.
Creating vector time with 25531 elements.
Creating vector temperature with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_0 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_1 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_2 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_3 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_4 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_5 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_6 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_7 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_8 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_9 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_10 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_11 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_12 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_13 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_14 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_15 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_16 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_17 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_18 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_19 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_20 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_21 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_22 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_23 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_24 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_25 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_26 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_27 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_28 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_29 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_30 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_31 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_32 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_33 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_34 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_35 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_36 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_37 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_38 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_39 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_40 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_41 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_42 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_43 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_44 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_45 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_46 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_47 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_48 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_49 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_50 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_51 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_52 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_53 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_54 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_55 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_56 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_57 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_58 with 25531 elements.
Creating vector time with 25531 elements.
Creating vector raw_59 with 25531 elements.
Creating vector time with 25531 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004211/2004.211.01/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/2004/2004211/2004.211.01/lopc.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/2004/2004211/2004.211.01/lopc.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/2004/2004211/2004.211.01/lopc.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/2004/2004211/2004.211.01/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.211.01.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_2004.211.01.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 12 segments.
[Warning: MATLAB has disabled some advanced graphics rendering features by
switching to software OpenGL. For more information, click <a
href="matlab:opengl('problems')">here</a>.] 
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_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_2004_211_01_211_01.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_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 = 112 Gridding with nix = 336, iZ = 199
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp470
[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 231)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   bbp676
[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 253)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   fl676_uncorr
[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 274)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   N
   BL
   BLflow
   LOPC
Only one good point or fewer - NaNing the gLOPCcount array.
                             - NaNing the gLOPCtransCount array.
                             - NaNing the gLOPCnonTransCount array.
                             - NaNing the gLOPCLCcount array.
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
  cvarname = gF
  cvarname = gB470
  cvarname = gB676
  cvarname = gBL
  cvarname = gBLflow
  cvarname = gLOPCcount
No valid data for gLOPCcount
  cvarname = gLOPCtransCount
No valid data for gLOPCtransCount
  cvarname = gLOPCnonTransCount
No valid data for gLOPCnonTransCount
  cvarname = gLOPCLCcount
No valid data for gLOPCLCcount
Encountered 0 NaN values in array of lon that is 126593 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 126593 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 119089 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 = 19933.204 since 1/1/1950
Looking for end   days = 19933.4992
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 24988.7708
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2004211_GulperTimes.txt && touch ../results/2004211_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/2004/2004211/2004.211.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004211/2004.211.01/syslog -startEsecs 1091076824.6033 -surveyName Dorado389_2004_211_01_211_01 >> ../results/2004211_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004211_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_gridded.mat

outvarstr =

    'gF gT gN gS gD gO gB470 gB676 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth '

2Column contouring gridded variable gD
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gT
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gS
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gN
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gO
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_2column.png
Elapsed time to save image: 10 seconds
Biolume contouring gridded variable gD
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gT
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gS
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gN
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gO
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB470
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB676
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gF
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gBL
  Drawing bottom contour from EM300 data
SWR image not added to the plot.
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_biolume.png
Elapsed time to save image: 35 seconds
2Column contouring gridded variable gLOPCcount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gLOPCtransCount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gLOPCnonTransCount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gLOPCLCcount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gT
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_lopc.png
Elapsed time to save image: 10 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 128)
  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_2004_211_01_211_01_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_2column.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_biolume.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_lopc.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_211_01_211_01_Temperature.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_01_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_211_01_211_01_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_01_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_211_01_211_01_Nitrate.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_01_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_211_01_211_01_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_01_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath);
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 Optical Backscatter @470 nm
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, 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 Optical Backscatter @676 nm
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, 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 Chlorophyll Fluorescence   
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_2004_211_01_211_01_Bioluminescence.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_01_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_01_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_01_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2004_211_01_211_01.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01.kml...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_211_01_211_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_2004_211_01_211_01.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
5 NaNs found in bbpRed.  Interpolating anyway.
1 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 117 NaN values in array of lon that is 15427 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 15310 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 15310 are not equal to number of Lat lon points = 15427
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_2004_211_01_211_01.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01.txt...
Copied to /mbari/AUVCTD/surveys/2004/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2004/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
5 NaNs found in bbpRed.  Interpolating anyway.
1 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_2004_211_01_211_01_decim.nc...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_211_01_211_01.nc...
Copied to /mbari/AUVCTD/surveys/2004/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2004/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_211_01_211_01.mat...
Copied to /mbari/AUVCTD/surveys/2004/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2004_211_01_211_01 processed" mccann@mbari.org < mail_Dorado389_2004_211_01_211_01.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.211.01.mat
Processing time: 117 seconds