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  • fastqc Exception (error)

    Hi,

    I am running the fastqc (v0.11.4) on Ubuntu 14.04.3 LTS.
    I have four fastq files (two pairs of paired-end reads samples). They are AFAIK from old solexa machines in sanger format
    somehow when I am trying to fastq the _1 files I get the following error message:

    Code:
    fastqc -t 12 -o ../Results/1c3c603f-29ac-4263-851d-b19f9ce4cfb0/fastqcResults/ 61627AAXX_1_1.fastq.gz 
    Started analysis of 61627AAXX_1_1.fastq.gz
    Exception in thread "Thread-1" java.lang.IllegalArgumentException: Unexpected cs char C
            at uk.ac.babraham.FastQC.Sequence.FastQFile.convertColorspaceToBases(FastQFile.java:334)
            at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:191)
            at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
            at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)
            at java.lang.Thread.run(Thread.java:745)
    than nothing happens.
    When I am using the same command for the _2 files, it works fine.

    Code:
    fastqc -t 12 -o ../Results/1c3c603f-29ac-4263-851d-b19f9ce4cfb0/fastqcResults/ 61627AAXX_1_2.fastq.gz 
    Started analysis of 61627AAXX_1_2.fastq.gz
    Approx 5% complete for 61627AAXX_1_2.fastq.gz
    ...
    I can't see any differences in the format of the two files.

    the header of the two files from one of the pairs looks like that:

    Code:
    zcat 61GAFAAXX_1_1.fastq.gz | head -n 12
    @SOLEXA12_1:1:1:990:4777/1 1:Y:0:0
    ..................................................
    +
    ##################################################
    @SOLEXA12_1:1:1:990:11674/1 1:Y:0:0
    ..................................................
    +
    ##################################################
    @SOLEXA12_1:1:1:990:17662/1 1:Y:0:0
    ..................................................
    +
    ##################################################
    and
    Code:
    zcat 61GAFAAXX_1_2.fastq.gz | head -n 12
    @SOLEXA12_1:1:1:990:4777/2 2:Y:0:0
    ..................................................
    +
    ##################################################
    @SOLEXA12_1:1:1:990:11674/2 2:Y:0:0
    ..................................................
    +
    ##################################################
    @SOLEXA12_1:1:1:990:17662/2 2:Y:0:0
    ..................................................
    +
    ##################################################
    Any ideas, why I can't run the _1 files?

    thanks
    Assa

    P.S.
    When I am running the SolexaQA++ tool, I can read all the four files without difficulties.

  • #2
    For reference, also posted (and possibly answered) on Biostars: https://www.biostars.org/p/167555/

    Comment


    • #3
      sorry about spamming the forum. I have wanted to delete the entries, but couldn't find any way to do so.

      Comment

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