# ATLAS / FAQ

• What to do in case of undefined reference to wrapper_dgemm_’ or similar Errors ?

Try to comment out the line #define ARMA_USE_WRAPPER in /usr/include/armadillo_bits/config.hpp

• How does ATLAS deal with indels?

Indels are influenced by alignment errors, which could stem from PMD, but this process has not been studied in enough detail for it to be modelled. There is thus no option to call indels with ATLAS. ATLAS ignores indels by not taking into account any base that is inserted into a read and by considering a reference base that is deleted in a read to not be covered by that read. It is advisable to run a local re-aligner over your BAM file before using ATLAS such that the number of mismatching bases is minimized across all the reads.

• Why do I get the error "Can not initialize post mortem damage function 'example_PMD_input_Empiric.txt': wrong format! Use either Skoglund[p,c], Exponential[a,b,c] or Empiric[0.2,0.3,...]"

If you want to use a PMD file created by ATLAS as PMD input, make sure you pass it with the parameter pmdFile and not pmd

• I am running recal and get the error message "ERROR: Issue solving JxF in RecalibrationEM::runNewtonRalphson()!". What does it mean?

You probably do not have enough data for the Newton-Raphson algorithm. Try using the entire X-chromosome if you are not already (or all available haploid data if you are not working with a male) and/or merge read groups.

• When I try to update with pull, I get the error message "fatal: repository 'https://vlink@bitbucket.org/phaentu/atlas.git/' not found"

You are probably updating an atlas directory that you cloned before Oct. 15 2018. We have since changed the directory breaking the link you used to clone atlas. Update the remote URL with:

cd atlas; git remote set-url origin 'https://vlink@bitbucket.org/WegmannLab/atlas.git/'
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