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uio-cels / NucDiff

In-depth characterization and annotation of differences between two sets of DNA sequences
Mozilla Public License 2.0
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ERROR: mummer and/or mg aps returned non-zero #16

Open Zhiliang-Zhang opened 4 years ago

Zhiliang-Zhang commented 4 years ago

Hi, I get a error message when ran command as following: nucdiff ../1D.fa ../chr1D_contig.fa . AK58VSCS

image

Could you give me some advices? Thanks!

Zhiliang

kseniakh commented 4 years ago

Hi,

Can you check if you can successfully run nucmer?

Zhiliang-Zhang commented 4 years ago

Hi,

Can you check if you can successfully run nucmer?

Hi, Thanks for your quick reply. I have tried nucmer and received error info. image

I installed NucDiff with bioconda: conda install -c bioconda nucdiff

Zhiliang

kseniakh commented 4 years ago

It is a problem with nucmer and not with NucDiff. One of the explanations can be a memory issue : https://sourceforge.net/p/mummer/mailman/message/34066860/.

Zhiliang-Zhang commented 4 years ago

It is a problem with nucmer and not with NucDiff. One of the explanations can be a memory issue : https://sourceforge.net/p/mummer/mailman/message/34066860/.

Thanks for your reply. I will change a large server and have a try.