DiffBind count function error related with BiocParallel and IRanges
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Entering edit mode
8 days ago
buffealo ▴ 130

I am getting the following error with counts <- dba.count(samples, bParallel=FALSE)

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Error in (function (cond)  :
error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in IRanges:::find_overlaps_in_groups_NCList(ranges(query), q_space, : 'q_groups' must be a CompressedIntegerList object

I tried running

library(BiocParallel)
register(SerialParam())

Before this attempt, I ran counts <- dba.count(samples) and the error was:

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Error processing one or more read files. Check warnings().
There were 17 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) :
  all scheduled cores encountered errors in user code
2:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
3:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
4:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
5:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
6:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
7:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
8:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
9:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
10:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
11:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
12:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
13:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
14:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
15:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
16:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors
17:   error in evaluating the argument 'x' in selecting a method for function 'assay': BiocParallel errors

I am stuck and looking forward to any help. Thank you

dba chipseq iranges diffbind • 178 views
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pls help, I need to solve this problem

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