Segmentaton fault with ART for simulating paried-reads

Question

[MEITUO]

ART/art_bin_MountRainier/art_illumina -ss HS25 -sam -i precision_dataset.fna -l 150 -f 1 -o art-paired-dat

    ====================ART====================
             ART_Illumina (2008-2016)          
          Q Version 2.5.8 (June 7, 2016)       
     Contact: Weichun Huang <[e-mail]> 
    -------------------------------------------

Segmentation fault

is anyone knows what is the error?

[GenoMax]

You can also use randomreads.sh from BBMap suite as an alternative if ART does not work.

[MEITUO]

i had used randomreads.sh, but it is quite slow if i want to get 10,000,000 reads, so i try to use other tools, whether these are more quickly

Answer 1

[Mensur Dlakic]

It is impossible to answer this definitively from the information you provided. I suggest you try this with a known DNA file, say a smallish bacterial genome, to make sure that there is nothing wrong with the simulator program itself. It that works as expected, the error most likely has to do with your input file precision_dataset.fna. I am guessing that it is either too big for your memory or improperly formatted.

[MEITUO]

thnaks, i will try to look at it