Get help
Despite our efforts to make the installation procedure as easy as possible, the variety of computers, operating systems, distributions and libraries make the installation outcome very difficult to predict. Should you have any problem, you might
- check issues reported on this page,
- ask your local administrator,
- open an issue,
- contact us.
Problems occurring during compilation
GSL
The Makefile has been written to match typical location for the installation of GSL on Linux and Mac OS X system. In case of different installation of the GSL, please edit CFLAGS and XLIBS in the Makefile. The online documentation of GSL provides a sample program. Try to compile this; it will give information on the correct setting of the flags.
Problems occurring during execution
Memory footprint
We work to keep the memory requirements at bay. Nevertheless, for large samples the required RAM might exceed 4 Gb. For example, a run of diri_sampler on a single window of 65000 reads from 454 required 4.1 Gb of RAM. If dec.py is used, this will run several jobs at the same time (parallelization), thus increasing the memory needs.
BAM files give me problems
We have heard from some users errors that might be due to colons : in the reference names.
reported by KMD
diri_sampler and memory leak
This seems to be solved now (thanks to Manuel Holtgrewe).
It happened that diri_sampler failed to run with a cryptic message that reads like: memory corruption: 0x0000000000. . . Usually, changing the name of the input file to something shorter was enough. For obscure reasons, it seemed to fail when the file name is 18 letter plus the suffix .far.
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