Error using Rsubread align: caugh segfault invalid permissions
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@gerard_llimos-10761
Last seen 5.3 years ago

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!

 

rsubread align segfault • 970 views
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Are you using the latest version of Rsubread? Could you please provide your session info (sessionInfo())?

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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

 

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Hi,

I am having this same problem with the lastest version of Rsubread for RNA-seq data. As in the original post, some fastq files work fine, others have this problem. Did anyone find a resolution?

R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /scalewlgpersistent/filesets/optnesi/CS400centos7bdw/imkl/2018.4.274-gimpi-2018b/compilersandlibraries2018.5.274/linux/mkl/lib/intel64lin/libmklgf_lp64.so

locale: [1] LCCTYPE=enNZ.UTF-8 LCNUMERIC=C
[3] LC
TIME=enNZ.UTF-8 LCCOLLATE=enNZ.UTF-8
[5] LC
MONETARY=enNZ.UTF-8 LCMESSAGES=enNZ.UTF-8
[7] LC
PAPER=enNZ.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enNZ.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] Rsubread_1.32.4

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Your Rsubread version is not the latest. The latest version is 2.0.0.

Your R is not up-to-date as well - the latest version is 3.6.

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Thank you! I apologize, I had only recently installed the package ans assumed I was working from the latest version. Upgrading the R and Rsubread install solved the issue!

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