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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering

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simreads long runtime

weilu1998 opened this issue · comments

commented

Hi,

I am wondering what's the expected runtime of simreads for 30X coverage and 300Mb genome? I generated the error profile using the top 20k reads from a Nanopore sequencing run and started the simread job 3 days ago and it is still running. I don't see any update to the log file. Is it expected? How to speed up the process?

Thanks

commented

Mmh thats not good. Please check the parameters for sure... Can you post the command?

Thanks
Fritz

commented

Hi @fritzsedlazeck,

Thanks for the reply!

SURVIVOR simreads ref.fa sample_error_profile.txt 30 sample_sim_rep1

This is the head of the error profile

Pos     P(stop) P(match)        P(mismatch)     P(ins)] P(del)
0       0.000000        0.639120        0.360880        0.000000        0.000000
1       0.000000        0.665107        0.334684        0.000070        0.000140
2       0.000000        0.650157        0.349563        0.000070        0.000210
3       0.000000        0.659658        0.325533        0.005169        0.009640
4       0.000000        0.660286        0.318477        0.009710        0.011526
5       0.000000        0.664827        0.311352        0.009780        0.014041
6       0.000000        0.665037        0.308977        0.012225        0.013762
7       0.000000        0.660496        0.316242        0.009291        0.013971
8       0.000000        0.658959        0.308488        0.013203        0.019350

This is the tail of the error profile

66885   0.999930        1.000000        0.000000        0.000000        0.000000
66886   0.999930        1.000000        0.000000        0.000000        0.000000
66887   0.999930        1.000000        0.000000        0.000000        0.000000
66888   0.999930        1.000000        0.000000        0.000000        0.000000
66889   0.999930        1.000000        0.000000        0.000000        0.000000
66890   0.999930        1.000000        0.000000        0.000000        0.000000
66891   0.999930        1.000000        0.000000        0.000000        0.000000
66892   0.999930        1.000000        0.000000        0.000000        0.000000
66893   0.999930        1.000000        0.000000        0.000000        0.000000
66894   0.999930        1.000000        0.000000        0.000000        0.000000