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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

  • check issues reported on this page,
  • ask your local administrator,
  • contact us at shorah@bsse.ethz.ch.

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.

getopt and optarg not declared

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 contain and freqEst. This is solved by adding the line 

#include <unistd.h>

at the beginning of both source files contain_src/contain.cc and freqEst_src/freqEst.cc.

Thanks to SL for pointing this out.

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.

I run s2f.py but it doesn't work

Did you follow our recommendation to run the experiments in a directory different from your installation one?

Now I can run s2f.py, but it says it can't find needle

Did you run make install and 

The license could not be verified: License Certificate has expired! Generate a Free license now.
 your EMBOSS installation?

 

BAM files give me problems

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_sampler and 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 .far.

bam2msa.py fails with a message like "TypeError: 'NoneType' object is not subscriptable when I run it on the files in sam_files

Try the following:

  1. download and unzip the attached file;
  2. align it to the HIV reference with novoalign -d HIV-ref.idx -o SAM -f HIV-1000.fastq > HIV-1000.sam;

  3. rerun samtools with samtools view -b -t HIV-ref.fasta HIV-1000.sam | samtools sort - S_1000;
  4. rerun bam2msa.py to extract the local window.