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Campbell.1933
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@campbell1933-11092
Last seen 8.3 years ago
Hi
I've been using Rsubread with a range of new and old FASTQ files and it has been working fine. The latest batch seems to be having some problems and for some of the files I get the following error after it crashes
Traceback:
1: .C("R_align_wrapper", as.integer(n), as.character(cmd), PACKAGE = "Rsubread")
2: align(index = "reference_index", minFragLength = 35, nthreads = 30, readfile1 = "RS-02239140_N3_DMSO_GFP_R1.fastq.gz", output_file = "RWPE.GFP.DMSO.3.BAM")
I think i saw an earlier post about 10 months ago with a similar issue but couldn't see a resolution.
I'm using Rsubread_1.22.2
Anyone got any thoughts?
thanks
Your post shows a function call but doesn't show any error message. What error message did you get? What you mean by "it crashes"?
AFAIK there are no unresolved issues with Rsubread unexpectedly stopping.
That was the error message and then it gives the options 1-4 for how to quit out of R. By crashes then i mean it doesn't do anything else. Maybe that's not the right word?
The output from traceback is not an error message, so you are keeping us completely in the dark as to what may have gone wrong for you.
Could you provide your commands and also the full screen output?
OK will do. I'm traveling so this will take a couple of days. thanks
The samples divided and run on Hiseq2500 v3 chemistry, high output flowcell, 100SE. The FASTQ files were then catenated.
R version 3.3.0 (2016-05-03) -- "Supposedly Educational" being run on a computer cluster.
In Rsubread
>align(index="reference_index", minFragLength=35, nthreads=30, readfile1="RS-02239142_N4_DMSO_input_R1.fastq.gz", output_file="RWPE.Inp.DMSO.1.BAM")
|| Threads : 30 ||
|| Phred offset : 33 ||
|| Min votes : 3 / 10 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41]
and then
|| The range of Phred scores observed in the data is [2,41] ||
....it runs for a while.....
*** caught segfault ***
address 0x7f3a5ee09fd0, cause 'invalid permissions'
Traceback:
1: .C("R_align_wrapper", as.integer(n), as.character(cmd), PACKAGE = "Rsubread")
2: align(index = "reference_index", minFragLength = 35, nthreads = 30, readfile1 = "RS-02239142_N4_DMSO_input_R1.fastq.gz", output_file = "RWPE.Inp.DMSO.1.BAM")
I suspect the problem might be related to the concatenation of your fastq files. Can you try to run align() on one of the fastq files before you merge them?
Yes, that was our thought too, but the non-concatentated file also failed
Could you provide us one of your fastq files in question so we can take a close look? Which reference genome did you use in your mapping?