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Question: Error using Rsubread align: caugh segfault invalid permissions
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gravatar for gerard_llimos
2.3 years ago by
gerard_llimos10 wrote:

Hi,

I am running Rsubread to align some RNA-seq data (paired end). I've tried some fastq files and it worked perfectly, however in some fastq it shoots me an error after a while (it starts the alignment but it stops always at the same position, i.e. 35%)  

The code is just this:

# Index
indexdirectory= "hg19index/hg19index"

#Alignment
align(index=indexdirectory,
      readfile1="uniquefastq/unique_C42_sh8_ETOH_1_R1.fastq.gz",
      readfile2="uniquefastq/unique_C42_sh8_ETOH_1_R2.fastq.gz",
      type="rna",
      input_format="gzFASTQ",
      output_file="C42_sh8_ETOH_1.bam",
      nthreads=12,
      phredOffset=33,output_format="BAM",unique=TRUE,indels=5,detectSV=F)

 

And the error is: 

 

35% completed, 28 mins elapsed, rate=10.0k fragments per second

*** caught segfault ***
address 0x7fa02e4202d0, cause 'invalid permissions'

Traceback:
1: .C("R_align_wrapper", as.integer(n), as.character(cmd), PACKAGE = "Rsubread")
2: align(index=indexdirectory, readfile1="uniquefastq/unique_C42_sh8_ETOH_1_R1.fastq.gz", readfile2="uniquefastq/unique_C42_sh8_ETOH_1_R2.fastq.gz", type="rna", input_format="gzFASTQ", output_file="C42_sh8_ETOH_1.bam", nthreads=12, phredOffset=33,output_format="BAM",unique=TRUE,indels=5,detectSV=F)
3: eval(expr, envir, enclos)
4: eval(ei, envir)
5: withVisible(eval(ei, envir))
6: source("RNAseq.R")

Possible actions:

....

 

How could I solve it? I guess that the problem might be in the fastq file.

Another question related to this, does the setting of phredOffset number have any influence on the output?

Thank you!

 

ADD COMMENTlink modified 2.3 years ago by Wei Shi2.9k • written 2.3 years ago by gerard_llimos10

Are you using the latest version of Rsubread? Could you please provide your session info (sessionInfo())?

ADD REPLYlink written 2.3 years ago by Wei Shi2.9k

Hello,

Thanks for the fast reply.

Yes, it is the new version:

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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

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

other attached packages:
[1] Rsubread_1.22.0

 

ADD REPLYlink written 2.3 years ago by gerard_llimos10
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