Error preprocessReads : Error in writeFastq
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Entering edit mode
@guillaumedachy-11994
Last seen 7 months ago
Brussels

Hello everyone !

I'm trying to preprocess paired-end reads in the QuasR Package, but I unfortunately get this error, which is surprising for me because that code worked on windows but not on linux (fedora). 

This could be a very naive question, and I apologize if it is... But thank you so much for helping me ! 

> infiles1 <- file.path("/run/media/ahmed/LACIE/RNAseq_Florence_JBD", c("RC_FA225_TTAGGC_R1.fastq.gz"))
> infiles2 <- file.path("/run/media/ahmed/LACIE/RNAseq_Florence_JBD", c("RC_FA225_TTAGGC_R2.fastq.gz"))
> outfiles1 <- paste(tempfile(pattern=c("output_1_")),".fastq",sep="")
> outfiles2 <- paste(tempfile(pattern=c("output_2_")),".fastq",sep="")
> resFA225 <- preprocessReads(filename=infiles1,
+                        filenameMate=infiles2,
+                        outputFilename=outfiles1,
+                        outputFilenameMate=outfiles2,
+                        nBases=0)
  filtering /run/media/ahmed/LACIE/RNAseq_Florence_JBD/RC_FA225_TTAGGC_R1.fastq.gz and
    /run/media/ahmed/LACIE/RNAseq_Florence_JBD/RC_FA225_TTAGGC_R2.fastq.gz
Error in writeFastq(chunks[filter], tmpOutputFilename, mode = mode, qualityType = "Auto",  :
  failed to write record 14

 

Does this give an idea to someone ?

Thank you very much !!

Guillaume

quasr rnaseq paired-end reads • 440 views
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