Depth assertion fail

[Thatguy027]

Hello,
I am running ALE on a number of samples and am getting this error for one sample:

ALE: ALElike.c:1678: computeDepthStats: Assertion `tempLogLike <= 0.0' failed.

Any idea how to go about fixing this issue?

Thanks

[robegan21]

Hi Stefan,
So I've never seen it throw that error before. If you want to share your data I can step through it in the debugger and see what in your data would be causing the problem (my best guess is an integer overflow somewhere, or the negative binomial function is returning NotANumber, but I do not see any obvious candidates. Otherwise you could replace line 1678 with a print statement to output the invalid values and continue:

if (tempLogLike <= 0.0) { printf("j=%d len=%d, depth=%f, GCpct=%d, negBinomParam_r[GCPct]=%f\n", j, contig->seqLen, contig->depth[j], GCPct, negBinomParam_r[GCpct]); continue; }

I might be able to figure out what is wrong with that print statement, and I imagine your results would not be too far off if there is just one or two lines that print.