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Daniel
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@daniel-24295
Last seen 3.4 years ago
So i've been trying to do some alignments with Rsub and every time i run it, only aligns one file and it doesn't do the rest. I have been running the latest version of everything, R( 4.0) Rsubread is 2.4.2 and BiocManager 1.30.10 The following code is from a tutorial for RNA-seq analysis but because of this problem, I can't replicate Code should be placed in three backticks as shown below
align(index="data/chr1_mm10",readfile1=fastq.files)
# //================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : SRR1552444.fastq.gz ||
|| Output file : SRR1552444.fastq.gz.subread.BAM (BAM) ||
|| Index name : chr1_mm10 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 3 / 10 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================= Running (02-Dec-2020 17:42:55, pid=4696) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Create the output BAM file. ||
|| Check the index. ||
The index was built by using an old version of Subread; its format is no longer supported. Please use the current version of the index builder to rebuild it.
# please also include the results of running the following in an R session
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rsubread_2.4.2 edgeR_3.32.0 limma_3.46.0
loaded via a namespace (and not attached):
[1] compiler_4.0.2 Matrix_1.2-18 tools_4.0.2 Rcpp_1.0.5 tinytex_0.27 grid_4.0.2
[7] locfit_1.5-9.4 xfun_0.19 lattice_0.20-41
Does anybody has an idea? ?I have 12 samples and it only returns one Thanks
Hi, Dan, I tried in my macOS to build a human chr1 index then map a small sample, and it was all done with no errors/warnings. In your case, because the align() function encountered an index problem, it stopped running, so the remaining 11 samples were not processed.
Can you try this:
, and copy the results here. This can tell if your index was correctly built.