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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
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
XLIBS in the Makefile.
New versions of the gcc compiler became more strict with respect to implicit declaration. Some users reported errors ('getopt' not declared in this scope) in the compilation of
freqEst. This is solved by adding the line
at the beginning of both source files
Thanks to SL for pointing this out.
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.
s2f.pybut it doesn't work
Did you follow our recommendation to run the experiments in a directory different from your installation one?
s2f.py, but it says it can't find
Did you run
make install and
We have heard from some users that they did not manage to extract a region from a BAM file using
bam2msa.py. The error might be something like
ValueError: invalid region ..... This might be due to colons (
:) in the reference names.
reported by KMD
diri_samplerand memory leak
It happens that
diri_sampler fails to run with a cryptic message that reads like: memory corruption: 0x0000000000...
Usually, changing the name of the input file to something shorter is enough. For obscure reasons, it seems to fail when the file name is 18 letter plus the suffix
bam2msa.pyfails with a message like "TypeError: 'NoneType' object is not subscriptable when I run it on the files in
Try the following:
align it to the HIV reference with
novoalign -d HIV-ref.idx -o SAM -f HIV-1000.fastq > HIV-1000.sam;
samtools view -b -t HIV-ref.fasta HIV-1000.sam | samtools sort - S_1000;
bam2msa.pyto extract the local window.