hanging when using large fasta files

[stefanoberri]

Hi.

I am experiencing an issue with wgsim 0.3

If I provide a human genome in fasta format everything wrks fine, however, if I provide a larger genome the program hangs indefinetly.

In particuar:

• the genome is a simulation of a cancer genome, so it is a tetraploid genome 4 copied of each chromosome for most chromosomes, with deletions and amplifications of some segments (about 11GB fasta file)
• each chromosome, has a different name.
• wgsim keep running 100% of the processor, but no reads are added to the fastq file
• no particular memory usage observed
• wgsim 0.2.3 (bundled with samtools) works fine with the large fasta file mentioned above

[s-edlund]

Stefan did you ever get this issue figured out? We're seeing similar behavior in version 0.3.1-r13. Thanks!

[luederm]

Having the same issue. My fasta file is only 11.7 MB. Hangs after the following output: [wgsim_core] calculating the total length of the reference sequence...

[luederm]

Got it to work by removing all 'N's from the reference

[AroneyS]

Presence of W, Y, R 'nucleotides' caused this for me.