jCounts produced Error in .local(x, use.names, use.mcols, ...)

I'm using v2.4.0 from bioconda. I could get the bin counts successfully though there are warnings like this for each sample.

Warning messages: 1: In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, : 700772 alignments with ambiguous pairing were dumped. Use 'getDumpedAlignments()' to retrieve them from the dump environment.

But the jCounts can't finish with the following message and error:

Junctions PJU completed Error in .local(x, use.names, use.mcols, ...) : For some pairs in 'x', the 2 alignments are not on the same chromosome. Cannot associate a unique genomic range to such pairs. Please call granges() with 'on.discordant.seqnames="drop"' to drop these pairs, or with 'on.discordant.seqnames="split"' to represent each of them with 2 genomic ranges in the returned GRanges object. Note that in both cases the returned object won't be parallel to 'x'. Alternatively, please consider using grglist() instead of granges() to turn 'x' into a GRangesList object instead of a GRanges object. See ?GAlignmentPairs for more information. In addition: Warning messages: 1: In .make_GAlignmentPairs_fromGAlignments(gal, strandMode = strandMode, : 700772 alignments with ambiguous pairing were dumped. Use 'getDumpedAlignments()' to retrieve them from the dump environment. 2: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''.

Here is my code: gbc <- gbCounts(features = features, targets = targets, minReadLength = minRL, maxISize = 50000, libType="PE") asd <- jCounts(counts = gbc, features = features, minReadLength = minRL, threshold = 5, minAnchor = 10, libType="PE")

If I set libType to SE, jCounts could work, but it's not right for my samples. I wonder why jCounts not works as gbCounts for the same samples. Thanks!

chernolab / ASpli

jCounts produced Error in .local(x, use.names, use.mcols, ...) #2