Execution of AUVprocess_main version 1.88 at 2025-04-09T20:50:37Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2025, ['098.01'], '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: 2025.098.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/navigation.nc')
Creating vector time with 448716 elements.
Creating vector mPos_x with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mPos_y with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mDepth with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mGpsNorth with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mGpsEast with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mGpsValid with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mPhi with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mTheta with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mPsi with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mOmega_x with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mOmega_y with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mOmega_z with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mPsaRange with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mAltitude with 448716 elements.
Creating vector time with 448716 elements.
Creating vector multibeamAltitude with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mDvlAltitude with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mEchoAltitude with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mEchoHorizRange with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mEchoAltitudeLast with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mEchoHorizRangeLast with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mEchoNumOfPings with 448716 elements.
Creating vector time with 448716 elements.
Creating vector nadirCnts with 448716 elements.
Creating vector time with 448716 elements.
Creating vector obstacleCnts with 448716 elements.
Creating vector time with 448716 elements.
Creating vector nGoodNadirBeams with 448716 elements.
Creating vector time with 448716 elements.
Creating vector medianNadirBeamNo with 448716 elements.
Creating vector time with 448716 elements.
Creating vector minBeamRange with 448716 elements.
Creating vector time with 448716 elements.
Creating vector minBeamCnts with 448716 elements.
Creating vector time with 448716 elements.
Creating vector thetaB with 448716 elements.
Creating vector time with 448716 elements.
Creating vector lsAlt with 448716 elements.
Creating vector time with 448716 elements.
Creating vector obstacleSlopeAlt with 448716 elements.
Creating vector time with 448716 elements.
Creating vector obstacleSlopeRange with 448716 elements.
Creating vector time with 448716 elements.
Creating vector obstacleAltAll with 448716 elements.
Creating vector time with 448716 elements.
Creating vector obstacleRangeAll with 448716 elements.
Creating vector time with 448716 elements.
Creating vector flightPathAngle with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mWaterSpeed with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mDvlValid with 448716 elements.
Creating vector time with 448716 elements.
Creating vector multibeamValid with 448716 elements.
Creating vector time with 448716 elements.
Creating vector multibeamFailed with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mDvlNewData with 448716 elements.
Creating vector time with 448716 elements.
Creating vector mDeltaT with 448716 elements.
Creating vector time with 448716 elements.
Creating vector nfix with 448716 elements.
Creating vector time with 448716 elements.
Creating vector efix with 448716 elements.
Creating vector time with 448716 elements.
Creating vector filter_north with 448716 elements.
Creating vector time with 448716 elements.
Creating vector filter_east with 448716 elements.
Creating vector time with 448716 elements.
Creating vector filter_depth with 448716 elements.
Creating vector time with 448716 elements.
Creating vector north_current with 448716 elements.
Creating vector time with 448716 elements.
Creating vector east_current with 448716 elements.
Creating vector time with 448716 elements.
Creating vector speed_bias with 448716 elements.
Creating vector time with 448716 elements.
Creating vector heading_bias with 448716 elements.
Creating vector time with 448716 elements.
Creating vector latitudeNav with 448716 elements.
Creating vector time with 448716 elements.
Creating vector longitudeNav with 448716 elements.
Creating vector time with 448716 elements.
Creating vector dNorthingTrn with 448716 elements.
Creating vector time with 448716 elements.
Creating vector dEastingTrn with 448716 elements.
Creating vector time with 448716 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/navigation.nc');
processNav(): median of positive valued depths = 47.6243
processNav(): Finding depths less than 476.2434 and times > 0
processNav(): length(Nav.depth) = 448716
processNav(): length(gindx)     = 448716
 
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/2025/2025098/2025.098.01/gps.nc')
Creating vector time with 9079 elements.
Creating vector hours with 9079 elements.
Creating vector time with 9079 elements.
Creating vector minutes with 9079 elements.
Creating vector time with 9079 elements.
Creating vector seconds with 9079 elements.
Creating vector time with 9079 elements.
Creating vector centiSeconds with 9079 elements.
Creating vector time with 9079 elements.
Creating vector latitude with 9079 elements.
Creating vector time with 9079 elements.
Creating vector longitude with 9079 elements.
Creating vector time with 9079 elements.
Creating vector quality with 9079 elements.
Creating vector time with 9079 elements.
Creating vector numberOfSatellites with 9079 elements.
Creating vector time with 9079 elements.
Creating vector hdop with 9079 elements.
Creating vector time with 9079 elements.
Creating vector antennaHeight with 9079 elements.
Creating vector time with 9079 elements.
Creating vector geoHeight with 9079 elements.
Creating vector time with 9079 elements.
Creating vector dgpsDataAge with 9079 elements.
Creating vector time with 9079 elements.
Creating vector dgpsRSID with 9079 elements.
Creating vector time with 9079 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/parosci.nc')
Creating vector time with 893509 elements.
Creating vector depth with 893509 elements.
Creating vector time with 893509 elements.
Creating vector temp with 893509 elements.
Creating vector time with 893509 elements.
Creating vector pressure with 893509 elements.
Creating vector time with 893509 elements.
Creating vector temp_period with 893509 elements.
Creating vector time with 893509 elements.
Creating vector pres_period with 893509 elements.
Creating vector time with 893509 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.34186 max(Depth.data) = 202.727
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.34186 max(Depth.data) = 202.727
 
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/2025/2025098/2025.098.01/hydroscatlog.nc')
Creating vector time with 358955 elements.
Creating vector Seconds with 358955 elements.
Creating vector time with 358955 elements.
Creating vector HundrethsOfSeconds with 358955 elements.
Creating vector time with 358955 elements.
Creating vector Snorm1 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector Snorm2 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector Snorm3 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector Gain_Status_1 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector Gain_Status_2 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector Gain_Status_3 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector RawDepthValue with 358955 elements.
Creating vector time with 358955 elements.
Creating vector RawTempValue with 358955 elements.
Creating vector time with 358955 elements.
Creating vector Temperature with 358955 elements.
Creating vector time with 358955 elements.
Creating vector ErrorValue with 358955 elements.
Creating vector time with 358955 elements.
Creating vector bb470 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector bb676 with 358955 elements.
Creating vector time with 358955 elements.
Creating vector fl676u with 358955 elements.
Creating vector time with 358955 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/ctdDriver.nc')
Creating vector time with 359064 elements.
Creating vector conductivity with 359064 elements.
Creating vector time with 359064 elements.
Creating vector temperature with 359064 elements.
Creating vector time with 359064 elements.
Creating vector cond_frequency with 359064 elements.
Creating vector time with 359064 elements.
Creating vector temp_frequency with 359064 elements.
Creating vector time with 359064 elements.
Creating vector spare with 359064 elements.
Creating vector time with 359064 elements.
Creating vector humidity with 359064 elements.
Creating vector time with 359064 elements.
Creating vector flow1 with 359064 elements.
Creating vector time with 359064 elements.
Creating vector CDOM with 359064 elements.
Creating vector time with 359064 elements.
Creating vector dissolvedO2 with 359064 elements.
Creating vector time with 359064 elements.
Creating vector salinity with 359064 elements.
Creating vector time with 359064 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/ctdDriver2.nc')
Creating vector time with 358934 elements.
Creating vector conductivity with 358934 elements.
Creating vector time with 358934 elements.
Creating vector temperature with 358934 elements.
Creating vector time with 358934 elements.
Creating vector cond_frequency with 358934 elements.
Creating vector time with 358934 elements.
Creating vector temp_frequency with 358934 elements.
Creating vector time with 358934 elements.
Creating vector flow2 with 358934 elements.
Creating vector time with 358934 elements.
Creating vector par with 358934 elements.
Creating vector time with 358934 elements.
Creating vector spare with 358934 elements.
Creating vector time with 358934 elements.
Creating vector salinity with 358934 elements.
Creating vector time with 358934 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/isuslog.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/2025/2025098/2025.098.01/isuslog.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/2025/2025098/2025.098.01/isuslog.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/2025/2025098/2025.098.01/isuslog.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 ISUS structure to NaN values.
 
Processing Biolume data...
[Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 71)
In processBiolume (line 21)
In processAUVmission (line 220)
In AUVprocess_main (line 227)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 71)
In processBiolume (line 22)
In processAUVmission (line 220)
In AUVprocess_main (line 227)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/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/2025/2025098/2025.098.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (7661 x 994) with 7615034 elements.
Creating matrix mepCountList (7661 x 994) with 7615034 elements.
Creating matrix countList (7661 x 994) with 7615034 elements.
Creating vector LCcount with 7661 elements.
Creating vector transCount with 7661 elements.
Creating vector nonTransCount with 7661 elements.
Creating vector ai_mean with 7661 elements.
Creating vector ai_min with 7661 elements.
Creating vector ai_max with 7661 elements.
Creating vector ai_std with 7661 elements.
Creating vector esd_mean with 7661 elements.
Creating vector esd_min with 7661 elements.
Creating vector esd_max with 7661 elements.
Creating vector esd_std with 7661 elements.
Creating vector countSum with 7661 elements.
Creating vector snapshot with 7661 elements.
Creating vector threshold with 7661 elements.
Creating vector sampleCount with 7661 elements.
Creating vector flowCount with 7661 elements.
Creating vector flowTime with 7661 elements.
Creating vector bufferStatus with 7661 elements.
Creating vector laserLevel with 7661 elements.
Creating vector counter with 7661 elements.
Creating vector counterPeriod with 7661 elements.
Creating vector laserControl with 7661 elements.
Creating vector countUnknownFrameCharacter with 7661 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7661 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7661 elements.
Creating vector flowSpeed with 7661 elements.
Creating vector countShortLFrameError with 7661 elements.
Creating vector countGarbledLFrame with 7661 elements.
Creating vector cFrameEsecs with 7661 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025098/2025.098.01/lopc.nc');
*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.098.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...
Reading: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.098.01.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 28 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.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_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 = 376 Gridding with nix = 1128, iZ = 402
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp420
   bbp700
   fl700_uncorr
   N
Only one good point - NaNing the gN array.
   BL
Only one good point or fewer - NaNing the gBL array.
   BLflow
Only one good point or fewer - NaNing the gBLflow array.
   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
No valid data for gN
  cvarname = gF
  cvarname = gB420
  cvarname = gB700
  cvarname = gBL
No valid data for gBL
  cvarname = gBLflow
No valid data for 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 437182 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 437182 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2025098_GulperTimes.txt && touch ../results/2025098_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/2025/2025098/2025.098.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2025/2025098/2025.098.01/syslog -startEsecs 1744133706.7445 -surveyName Dorado389_2025_098_01_098_01 >> ../results/2025098_GulperTimes.txt
Executing: removeGulpDups.py ../results/2025098_GulperTimes.txt
Bottle: 0 Time: 1744174461.1426 Depth: 200.0358 Dist: 54.1584
Bottle: 1 Time: 1744174607.9226 Depth: 149.8956 Dist: 54.3204
Bottle: 2 Time: 1744174853.1358 Depth: 59.989 Dist: 54.5982
Bottle: 3 Time: 1744174942.5396 Depth: 29.9892 Dist: 54.7103
Bottle: 4 Time: 1744174986.3366 Depth: 19.9979 Dist: 54.7633
Bottle: 5 Time: 1744175021.3443 Depth: 9.9712 Dist: 54.797
Bottle: 6 Time: 1744175061.7415 Depth: 0.016295 Dist: 54.8336
Bottle: 7 Time: 1744203598.7366 Depth: 200.0167 Dist: 90.1296
Bottle: 8 Time: 1744203742.7367 Depth: 149.9439 Dist: 90.2898
Bottle: 9 Time: 1744203981.9403 Depth: 59.9716 Dist: 90.5599
Bottle: 10 Time: 1744204065.9346 Depth: 29.9422 Dist: 90.6562
Bottle: 11 Time: 1744204107.3417 Depth: 19.978 Dist: 90.7044
Bottle: 12 Time: 1744204153.5386 Depth: 9.9773 Dist: 90.7507
Bottle: 13 Time: 1744204199.7354 Depth: -0.1819 Dist: 90.7923
Bottle: 14 Time: 1744218852.9416 Depth: 150.0065 Dist: 109.9526
Bottle: 15 Time: 1744219090.7353 Depth: 59.9442 Dist: 110.2195
Bottle: 16 Time: 1744219183.139 Depth: 29.9858 Dist: 110.3272
Bottle: 17 Time: 1744219226.336 Depth: 19.9758 Dist: 110.3758
Bottle: 18 Time: 1744219255.144 Depth: 9.9106 Dist: 110.4117
Bottle: 19 Time: 1744219288.3418 Depth: 0.089723 Dist: 110.4485
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_gridded.mat

outvarstr =

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

2Column contouring gridded variable gD
  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.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_2column.png
Elapsed time to save image: 8 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.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_biolume.png
Elapsed time to save image: 28 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.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_lopc.png
Elapsed time to save image: 8 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_2column.png...
Copied to /mbari/AUVCTD/surveys/2025/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_biolume.png...
Copied to /mbari/AUVCTD/surveys/2025/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_lopc.png...
Copied to /mbari/AUVCTD/surveys/2025/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2025/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2025/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2025/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2025-04-08T17:35:06Z
gmtstr(tend) = 2025-04-09T18:30:50Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
20 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_decim.nc...
Copied to /mbari/AUVCTD/surveys/2025/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing KML files ...
KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Creating Dorado389_2025_098_01_098_01.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01.kml...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_098_01_098_01_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 445)
In build_auv_survey (line 530)
In AUVprocess_main (line 257)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2025-04-08T17:35:06Z
gmtstr(tend) = 2025-04-09T18:30:50Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
20 NaNs found in bbpRed.  Interpolating anyway.
Encountered 1154 NaN values in array of lon that is 44872 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 43718 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 43718 are not equal to number of Lat lon points = 44872
AUV track probably goes outside of the range of the .grd file being used.   Setting bottom depths to 1000 m
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01.txt...
Copied to /mbari/AUVCTD/surveys/2025/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2025/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing netCDF file ...
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01.nc...
Copied to /mbari/AUVCTD/surveys/2025/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2025/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_098_01_098_01.mat...
Copied to /mbari/AUVCTD/surveys/2025/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
./permalink_url.sh http://dods.mbari.org/cgi-bin/nph-nc/data/auvctd/surveys/2025/netcdf/Dorado389_2025_098_01_098_01.nc
 
 
*************************************************************************
Composing email to send to auvctd@listserver.mbari.org ...
!mail -s "Survey Dorado389_2025_098_01_098_01 processed" auvctd@listserver.mbari.org < mail_Dorado389_2025_098_01_098_01.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.098.01.mat
Processing time: 184 seconds