Bismark_methylation_extractor problem

[blancha]

--scaffolds/--gazillion  Users working with unfinished genomes sporting tens or even hundreds of thousands of
                         scaffolds/contigs/chromosomes frequently encountered errors with pre-sorting reads to
                         individual chromosome files. These errors were caused by the operating system's limit
                         of the number of filehandle that can be written to at any one time (typically 1024; to
                         find out this limit on Linux, type: ulimit -a).
                         To bypass the limitation of open filehandles, the option --scaffolds does not pre-sort
                         methylation calls into individual chromosome files. Instead, all input files are
                         temporarily merged into a single file (unless there is only a single file), and this
                         file will then be sorted by both chromosome AND position using the Unix sort command.
                         Please be aware that this option might take a looooong time to complete, depending on
                         the size of the input files, and the memory you allocate to this process (see --buffer_size).
                         Nevertheless, it seems to be working.

[Brian Bushnell]

The easiest workaround is to increase your file handle limit, if it's not already at the max.

[drdna]

I am getting the following error running bismark_methylation_extractor:

bismark_methylation_extractor --bedGraph --counts SS116_S1_L001_R1_001.fastq.gz_bismark_bt2_pe.bam
.......
Failed to open filehandle: Too many open files at /opt/bismark_v0.14.5/bismark2bedGraph line 266, <IN> line 145753.

My guess is that the program is only designed to work with "nice" reference genomes where the assemblies consist of just a few chromosomes (scaffolds).

Aside from concatenating multiple scaffolds and deconvoluting the results afterward, does anyone know of a work-around?