Rsubread crash on Mac during alignment
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raf4 ▴ 20
@raf4-8249
Last seen 16 months ago

Dear Bioconductor Forum,

Rsubread crashed on my 32Gb Mac on a particular pair of fastq files. It worked fine on the previous file in the dataset and also other times I had used it. The CPU was at 100% and the memory was at 24.3% all the way through the run. The script was

library(Rsubread)
align(index="GRCh38",readfile1="a2-Solub-W2_S1_L001_R1_001.fastq.gz",readfile2="a2-Solub-W2_S1_L001_R2_001.fastq.gz",output_file="a2-Solub.bam")

The command line and error message was:

c2b2afmd2:GrCh38 friedman$ R CMD BATCH align2SC.R
/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60:  4665 Abort trap: 6           ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

Here is the last line of the *.Rout file

||   70% completed,  90 mins elapsed, rate=3.7k fragments per second          ||

(I am not reproducing the whole file for space).

It stopped at this point, in each of 3 runs.

The sessionInfo() (obtained from the GUI) is:

 

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.4

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] Rsubread_1.24.1

loaded via a namespace (and not attached):
[1] tools_3.3.2

Please advise.

Thanks and best wishes,

Rich

Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)

 

software error rsubread • 833 views
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Dear Rich, could you please send us the fastq files under question so we can take a close look? Thanks, Wei

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xu • 0
@xu-12377
Last seen 4.4 years ago

Hi, I have similar R crash issues. After around 10 minutes, the program crashed.

The fastq files (ChIP-seq, from mouse) are from Ion Torrent machine.

At first I used MAC, then I used our Linux rstudio server, where the CPU and memory are much better.

I also tried the Subread running in Linux, crash all the same.

Then I tried my old data from Arabidopsis with Ensembl tair10 genome, crash all the same.

When I used Rsubread v1.18, there is not problem, so before solving this problem, can I use the data from v1.18

Thank you!

Xu

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

Dear Richard, thanks for sending us your data. This should be fixed it in the latest version (1.24.2) - it runs well on our Macbook.

Wei

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raf4 ▴ 20
@raf4-8249
Last seen 16 months ago

Dear Wei and Yang,

I am sorry that I didn't get back to you. The person whom I was helping when I found the bug went elsewhere.

I am curently using the new version and it works fine.

Thanks and best wishes,

Rich

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Thanks for letting us know Rich!

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