Error caused by large input file

[xxTAT]

Hi, I'm having some problems using the following code：

clusteredCds = clusterrnaCrosslink(cds = cds,
cores = 25,
stepCount = 2,
clusterCutoff = 100)

My input file size is 2.5Gb. It seems to be too large, causing the following error message to appear during clustering.

Error in .Call2("C_validate_Ranges", x_start, x_end, x_width, PACKAGE = "IRanges") :
long vectors not supported yet: memory.c:3888

I hope you can help me solve this problem. Thank you very much.

[JLP-BioInf]

Yes no poblem, it should be fine with that. How many RNAs do you have in the object? could you show the output of topTranscripts(cds) please

[xxTAT]

OK. Thank you again.
The last time I combined the two results, the input file size was 2.5Gb. This time I'll do two duplicates separately, and the input file size is 1.25Gb. Here's the result of topTranscripts. c1 is a fictitious file of mine.

topTranscripts(cds)
RNA type c1 s1 samples control
1 virus_rna intra 2 6610322 6610322 2

[JLP-BioInf]

O.K this looks fine, and you are still receiving the same error? I would always try and run the second sample with at least some of the reads in there. Take a head of 2000 from "s1" and make that "c1" if there is not enough to cluster (2 reads) sometimes you can get odd behaviour.

[JLP-BioInf]

Can i close the issue?

[xxTAT]

hi, i try rnaCrosslinkOO again. In this time, i choice a small rna for structure prediction. In Fold step, i receive following news. ERROR: Supplied structure constraints create empty solution set for sequence. But I still get the predicted structure. Does it mean that i get the right structrue? Finally, thank you for you help. Best wish!