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Common errors
=============
**Error: unable to find any alignments to process**
- Have you run the align stage? If not, run it.
- If you have run the align stage, have the alignments worked? Have a
look inside sample/last/pass/2D or appropriate. If there are files
there, but they are 0 bytes, see below.
**All my LAST alignment files are empty**
- Have you indexed your reference file?
**lastal: invalid option -- 'o' when aligning**
- This means your version of LAST is too old. Older versions do not
support the -o option to output to a file and only output to the
screen.
- Solution: install latest version of LAST.
**I don't get a PDF file in the latex directory**
- If there is a .tex file, then something went wrong converting the
LaTeX to PDF - probably missing LaTeX packages.
- Have a look at the .log file inside the latex directory. You will
likely see an error such as:
`` ! LaTeX Error: File `multirow.sty' not found. ``
- In this instance, you need to install the multirow package.
**java.lang.OutOfMemoryError: Java heap space**
- Try editing the line in the nanook file of the bin directory: JAVA\_ARGS="-Xmx2048m"
- By default, this sets a maximum Java memory size of 2048 Mb - try increasing this according to what your memory you have available.
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