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.