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thread 'main' panicked, "index out of bounds: the len is 10 but the index is 10" #244
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Hello @lucy924, Could you send me the whole panic message? |
Hi @ArtRand
|
Hello @lucy924, thanks for sending the traceback. I'll have a build to you with the fix asap. |
Hello @lucy924, What you're doing looks reasonable to me. With respect to this error:
If for some reason bedMethyl records from the 'b' sample are systematically failing you cold see zero records being sampled and these errors will be in the log. Looks like you have |
Hi @ArtRand I went through a bunch of the logs and none of them give any actual error messages, they just stop with the last line
Unfortunately the mCG DMR logs were deleted somewhere along the way, but if you need them I can rerun it at some point. |
Hello @lucy924, Thanks for sending the logs over. Do other chromosomes 6mA DMR seem to work and just chr14 is having problems? One thing I noticed is that you use Sorry for the somewhat cryptic asks, I have a theory for what's going on, but I need a little more information. Thanks. |
Hi @ArtRand Thanks for the clarification on the A/T - I wasn't entirely sure from the docs so put T down just in case, figuring it wouldn't do any harm. Other than chrY, I had the same problem with one sample, I set On mCG
6mA is behaving weirdly on all samples this time, and I don't think I've done anything different. Unfortunately I don't have time this week to delve into it more, I'll let you know if I figure out what happened. I've attached example outputs for both mCG and 6mA, hopefully it helps ... I managed to get good outputs using the below (both B and C sets):
And I'm running with this data for now, do you think it likely that issues happened with the same samples on chr14 and the problems are just hidden in this case? Thanks, |
Hello @lucy924, I've made a refactor to how the tabix indices are handled in |
Hi @ArtRand |
Hi,
I've had this issue cropping up in some of my dmr's but not consistently.
I'm looping through each of my paired samples and each chromosome reference (human T2T), with different pileups (one using the
-traditional
preset and another using-cpg
.The samples are of differently treated cancer cell lines that have been whole genome sequenced.
experiment names:
B3, C3, B4, B5, C5, B6, C6
Problem pileup, pair, chromosome so far:
Do you think rerunning these specific pileups will help?
Pileup code
DMR code
Maybe related issue
I'm not sure if this next issue related but I'm also getting a different error with other pairs as well:
This is the list of experiments with not enough datapoints
I initially didn't think this was a problem, (especially as the B experiments are a female derived cell line) but then I started getting the same error on autosomal chromosomes too, in which the alignment depth might not be great but I didn't think it was this bad.
Appreciate any insights!
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