File not found error when using dupRadar::analyzeDuprates
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b.nota ▴ 340
@bnota-7379
Last seen 12 months ago
Netherlands

I am trying to use dupRadar on bam files, but get an Rsubread error. However, Rsubread is properly installed and no errors there. Is this a bug? Here my code:

library(dupRadar)

bamDuprm <- markDuplicates(dupremover="picard",
               bam="Sample01Aligned.sortedByCoord.out.bam",
               path="~/picard-2.17.6",
               rminput=FALSE)

# The call parameters:
bamDuprm <- "Sample01Aligned.sortedByCoord.out_duprm.bam"    # the duplicate marked bam file
gtf <- "~/Reference/mm10/Mus_musculus/Mus_musculus.GRCm38.92.gtf"  # the gene model
stranded <- 0       # '0' (unstranded), '1' (stranded) and '2' (reversely stranded)
paired   <- FALSE   # is the library paired end?
threads  <- 20       # number of threads to be used

# Duplication rate analysis
dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file './.Rsubread_featureCounts_pid17093': No such file or directory

But Rsubread is installed:

library(Rsubread)
featureCounts()
NCBI RefSeq annotation for mm10 (build 38.1) is used.
Error in paste(files, collapse = ";") :
  argument "files" is missing, with no default

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rsubread_1.26.1 dupRadar_1.6.0

loaded via a namespace (and not attached):
[1] compiler_3.4.4 tools_3.4.4

Anyone seen this before? Any solutions? Thanks.

dupradar rsubread • 612 views
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I thought originally that Rsubread doesn't make the file that is mentioned in the error message, but it turns out that it does. See Wei Shi's answer below.

If you install R 3.5.1 and the latest version of Bioconductor, the code should run fine.

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Thank you, I think it is the tilde (~) in my path name. I thought R would understand that.

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Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 1 day ago
Australia/Melbourne/Olivia Newton-John …

This file path issue has been fixed in the recent Rsubread releases. Please update your Rsubread and R to their latest. The latest Rsubread version is 1.30.5.

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Thank you, I will check the newest version.

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