I downloaded L0 MODIS files (Terra and Aqua) from LAADS and processed them into L1A/GEO in Seadas. After this I was going to process with already working script with the next work-flow: L1A extraction-> L1B-> L2. But I have very strange problem now: I can not subset Aqua L1A files, after running the script (via Seadas GUI I have the same story) I have the next mistake:

"lonlat2pixline 2006109.1100_A.GEO 15.5 54.1 22.5 58

lonlat2pixline 100% done. Reading scan: 1500 out of 1959
modis_L1A_extract.csh: ERROR: lonlat2pixline failed to determine start/end line/pixel. Exiting."

With MODIS Terra files from the same source, after the same processing everything works well..

Is this a problem of L0 files or processing from L0 to L1A ??
Absolutely unexpected problem...

Thank you

Try opening the L1A file in SeaDAS and verify with Functions->Cursor Position that the region you are specifying exists in the file. The region you specify appears to be around the Arabian Sea.

This is a boundary of the region of Baltic Sea (Central and Southern part: SWLON SWLAT NELON NELAT), and with absolutely SAME script with the same boundaries, but with Terra images it works normally..
I opened L1A in Seadas, and yes, this is a correct region (I can see the Baltic there), but in cursor position window I don't see the lat/lon coordinated. Is it normal?
I have no Ideas what to do...

Sorry, my mistake about the region. When you open the L1A file in SeaDAS make sure you also specify the GEO file that corresponds to this L1A file. Also, I'm guessing you created the GEO file using SeaDAS? If so, try creating it again and look at the command output to make sure the geo check step at the end reports around 100% valid pixels.

With checking GEO file it was Ok, but I tried to check it again, and processed one file again from L0 to L1A, and it seems OK:
"Number of pixels with missing geolocation: 0
Percent of geolocated pixels (rounded): 100"

But when I open this L1A it shows absolutely wrong coordinates - something like 29/-12 where it should be about 21/54.5.. What can be the reason for this wrong geo-coding?

I downloaded now one L0 file for one of the same granule from OC website, and processed it to L1A - and everything is OK with geolocation.
But with that LAADS L0 I have that wrong geolocation problem.. Is there any significant difference between L0 files from LAAD and OC? I used L1A files from LAADS for ocean colour processing, and had no problems before. But now it seems quite strange. And even more strange that this problems are only with Aqua files (and 1 or 2 Terra also, but with all Aqua files I have - about 150)

I have no idea why LAADS L0 files wouldn't work. They should be the same as our L0 files. Can you make one of the L0 LAADS files available for me to download? If not can you tell me the name and I'll try to get it myself from LAADS.

I already deleted all these bad L0 files. You can try to download for example this one: MYD00F.A2006135.1140.005*, search by filename.
I have already downloaded part of these L1A files for the same scenes, and it seems they work normally, at least all the processing until L2 is going well.

I searched for that pattern at http://ladsweb.nascom.nasa.gov/data/names.html and no products were found for Collection 5.0 or 5.1.

Sorry, try MYD00F.A2006135.1140*, without "005". It will find the file

I processed MYD00F.A2006135.1140.20061351452.001.PDS with no problems. The data with navigation appeared to display correctly and lonlat2pixline gave:

  $ lonlat2pixline A2006135114000.GEO 15.5 54.1 22.5 58
  Input file A2006135114000.GEO is MODIS Aqua Geolocation Fields.

  lonlat2pixline 100% done. Reading scan: 1500 out of 1959
  # 287 754 136 648
  sline=136
  eline=648
  spixl=287
  epixl=754

If you want to continue investigating this problem, please re-download and reprocess the file in this manner:

  modis_L0_to_L1A_GEO.csh MYD00F.A2006135.1140.20061351452.001.PDS -satellite aqua
  lonlat2pixline A2006135114000.GEO 15.5 54.1 22.5 58