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cbg-ethz / PredictHaplo

This software aims at reconstructing haplotypes from next-generation sequencing data.
GNU General Public License v3.0
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Closed AndreaAguadoM closed 2 years ago

AndreaAguadoM commented 2 years ago

Hello

I downloaded this tool from bioconda, but when trying to use it over my sample, the following error appears:

prefix = AND19006 cons = reference.fasta visualization_level = 1 FASTAreads = AND19006.sam have_true_haplotypes = 0 FASTAhaplos = do_local_Analysis = 1 After parsing the reads in file AND19006.sam: average read length= -nan 0 First read considered in the analysis starts at position 100000. Last read ends at position 0 There are 0 reads Segmentation fault (core dumped)

This is the command line that I wrote so PredictHaplo could be executed:

predicthaplo --sam AND19006.sam --reference reference.fasta --prefix AND19006 --have_true_haplotypes 0

Is there someone who can help me? Thanks in advance!

kpj commented 2 years ago

The bioconda version and the master branch of this repository are quite out-of-sync. Could you rerun your analysis with the latest version (from this repository) and check if the error disappears?

AndreaAguadoM commented 2 years ago

Yes! it has dessapeared, thank you!