Cannot import a BLAST file into MEGAN5
Entering edit mode
7.5 years ago

Hi all,

After running a command-line blast (23S rRNA plastid sequences) against a custom target database (sequences downloaded from NCBI), I wanted to visualize my BLAST results in MEGAN (as I had previously done in the past).

When trying to import a blast file (.blastn) into MEGAN, however, I get prompted with the following error message Line 1: ';' expected, got: 's' 

and I have no idea what is wrong with my input.

I first thought it might be a compatibility issue with the MEGAN software as I had a somewhat old version so I downloaded the latest one (MEGAN5 v.5.3.0) but I still get the same error message. I visualized my .blastn file in a text editor to make sure that it was fine as the error message makes it seem as if I have a syntax error but it does seem fine. I even tried a regular BLAST online with the NCBI BLAST but MEGAN also won't even open this file (.xml).

The weirdest thing is that when opening the file with MEGAN on a friend's laptop, it works fine so I'm assuming that there is something wrong with my computer but I have no idea how to solve this issue after reinstalling the MEGAN software.

I am currently running the latest version of MEGAN5 v.5.3.0 on a windows 7 (x64) laptop.

Any thoughts?


Blast-file MEGAN Metagenome rRNA • 2.7k views
Entering edit mode

What locale is set on your computer by default? I had a similar problem, but not with MEGAN using Ubuntu set to French -- in that case java wasn't able to process delimiters properly. You can set your locale in command line, java -Duser.language=en; also, there could be problem with line endings as linux/windows have them defined somewhat differently.

Entering edit mode

Thanks Pavel,

I think you might be right regarding my Java compatibility with the "French language". I however managed to solve my issue by changing the name of my working directory. For whatever the (stupid) reason, I had named it with a " 's" in the title and I think that Java did not like this (i.e. was not able to actually find my input files). Renaming it without the " 's" did it though.

Thanks again, Guillaume.

Entering edit mode

Good to know that it is solved!


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