Unix-based operating systems, including Apple OSX and Linux, limit how many files may be open at a time. This includes not just the visible files, but all of the various temporary hidden files that are used behind the scenes by Geneious, the operating system and any other software running on your computer.
You may encounter this error when you are running assemblies using large numbers of reference sequences. For example, this error may occur when assembling RNAseq NGS data against a large number of reference transcripts, as Geneious requires several open files per reference sequence.
By default, the maximum number of files that Mac OS X can open is set to 12,288 and the maximum number of files a given process can open is 10,240.
For Linux OS’s the maximum number of files may vary depending on the “flavour” of Linux.
There are two solutions to fix this error:
1. Reducing the number reference sequences
You can decrease the number of open files required by Geneious by concatenating a list of reference sequences into one sequence. This can be done by selecting a single list and going Geneious Menu Tools -> Concatenate sequences and alignments. Provided your references are annotated, post assembly you will be able to use the coverage map combined with the annotation information to identify which transcripts your RNAseq reads are assembling against.
We recommend using the option to add poly-N spacers. This will ensure does the assembler does not map reads wrongly across adjacent transcripts, and also, this should assist with mapping of post-transcriptional additions.
Note that the concatenation tool in Geneious R8 and earlier has poor performance when used for 10,000 or more sequences. This has been fixed in Geneious R9 and later.
2. Altering the System default settings
You can alter the default “open file” limits for your operating system. We provide the following links with instructions on how to do this, but use at your own risk!