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Question: RNA Seq // QuasR : Error while extracting unmapped reads
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gravatar for guillaume.dachy
6 days ago by
Brussels
guillaume.dachy0 wrote:

Hi everyone,

I'm trying to use QuasR since weeks now for his precious function allowing to align an auxiliary genome, but I get some trouble which are maybe very naive ... but hard to resolve for me ! 

Does this following error message does an idea to someone ? 

> file.copy(system.file(package="QuasR", "extdata"), ".", recursive=TRUE)
[1] TRUE
> sampleFile <- "extdata/samples_rna_paired_copie.txt"
> genomeFile <- "BSgenome.Mmusculus.UCSC.mm10"
> auxFile <- system.file(package="QuasR", "extdata", "auxiliaries_copie.txt")
> proj <- qAlign(sampleFile, genome=genomeFile, auxiliaryFile=auxFile, splicedAlignment=TRUE)
alignment files missing - need to:
    create 2 auxiliary alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
PC-113-219 
         1 
Performing auxiliary alignments for 2 samples. See progress in the log file:
C:/Users/gdachy/Documents\QuasR_log_15ec5fec2268.txt
Error in checkForRemoteErrors(val) : 
  one node produced an error: Error on PC-113-219 processing sample F:/RNAseq/RC_FA225_TTAGGC_R1.fastq.gz : Error while extracting unmapped reads (return value: -45599932)

 

I didn't find anything similar on the forum... 

Thank you very much for your help !! 

Regards,

Guillaume 

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