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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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simreads endless runtime #208

Open bjhunt-git opened 4 months ago

bjhunt-git commented 4 months ago

Hi, I seem to have the same issue as described here in that simreads just seems to run without ever completing - my current run has been going for 5 days. This is a ~400Mb genome, and I'm using SURVIVOR version 1.0.7.

I used this command to generate an error profile from the alignment of ONT reads against the genome

samtools view -s 0.1 HMW_127_minimap.sorted.bam | SURVIVOR scanreads 1000 HMW_127_error_profile.txt

Then used the error profile in conjunction with the genome like so:

SURVIVOR simreads genome.fasta HMW_127_error_profile.txt 20 006_sim

The head of my error profile looks like this:

Pos P(stop) P(match)    P(mismatch) P(ins)] P(del)
0   0.000000    0.999999    0.000000    0.000000    0.000001
1   0.000001    0.999998    0.000000    0.000002    0.000001
2   0.000001    0.985211    0.014777    0.000007    0.000006
3   0.000001    0.975655    0.011524    0.005442    0.007379
4   0.000001    0.971914    0.011896    0.006624    0.009565
5   0.000001    0.963356    0.015773    0.008418    0.012453
6   0.000001    0.958994    0.016409    0.010166    0.014431
7   0.000001    0.955781    0.016698    0.011152    0.016368
8   0.000001    0.952985    0.017912    0.011795    0.017307
9   0.000001    0.950113    0.019279    0.012421    0.018187
10  0.000001    0.948899    0.019375    0.012848    0.018879

And the tail like this:

56070   0.999999    1.000000    0.000000    0.000000    0.000000
56071   0.999999    1.000000    0.000000    0.000000    0.000000
56072   0.999999    1.000000    0.000000    0.000000    0.000000
56073   0.999999    1.000000    0.000000    0.000000    0.000000
56074   0.999999    1.000000    0.000000    0.000000    0.000000
56075   0.999999    1.000000    0.000000    0.000000    0.000000
56076   0.999999    1.000000    0.000000    0.000000    0.000000
56077   0.999999    1.000000    0.000000    0.000000    0.000000
56078   0.999999    1.000000    0.000000    0.000000    0.000000
56079   0.999999    1.000000    0.000000    0.000000    0.000000

Any advice would be much appreciated - thank you.