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  • Error while running bcl2fastq

    Hello,

    I did install the bcl2fastq as mentioned in the post. However when I am running it I am getting following error. Can anyone help me to resolve this?

    I used the following script in bold

    /usr/local/bin/configureBclToFastq.pl --input-dir /media/gastrula/2TB/transcriptome/SG002_07122016/161207_D00239_0187_AHWM2FBCXX/Data/Intensities/BaseCalls --output-dir ./ Unaligned --sample-sheet /media/gastrula/2TB/transcriptome/SG002_07122016/161207_D00239_0187_AHWM2FBCXX/Data/Intensities/BaseCalls/SG002_07122016_PoolA_rep1_samplesheet.csv

    Error is:

    "my" variable $value masks earlier declaration in same statement at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 760.
    syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 747, near "$variable qw(ELAND_FASTQ_FILES_PER_PROCESS)"
    Global symbol "$variable" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 749.
    syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 751, near "$directory qw(ELAND_GENOME)"
    Global symbol "$self" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$directory" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$project" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$sample" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$lane" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$barcode" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$reference" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
    syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 761, near "}"
    /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm has too many errors.
    Compilation failed in require at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
    BEGIN failed--compilation aborted at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
    Compilation failed in require at /usr/local/bin/configureBclToFastq.pl line 250.
    BEGIN failed--compilation aborted at /usr/local/bin/configureBclToFastq.pl line 250.

  • #2
    @saupra: I moved your post to a new thread.

    Have you validated this install of bcl2fastq? I think there is a small test flowcell included in the software (if I recollect).

    Comment


    • #3
      Det Genomax,

      I haven't. Actually I am doing for the fist time. Could you help me to perform this test?

      Comment


      • #4
        There are a couple of test flowcells included in bcl2fastq distribution (bcl2fastq/data/share/examples/Validation). You can test using those. Directions on how to use those cells are likely in the install document.

        Comment


        • #5
          Dear Genomax

          I think there is some issue with the installation only i used the following command
          /usr/local/bin/configureBclToFastq.pl --input-dir /media/gastrula/2TB/biotools/bcl2fastq/data/share/examples/Validation/100723_EAS346_0188_FC626BWAAXX_120418 --output-dir /output

          and still getting same error. Can you help me to figure out what could be done next?


          "my" variable $value masks earlier declaration in same statement at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 760.
          syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 747, near "$variable qw(ELAND_FASTQ_FILES_PER_PROCESS)"
          Global symbol "$variable" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 749.
          syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 751, near "$directory qw(ELAND_GENOME)"
          Global symbol "$self" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
          Global symbol "$directory" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
          Global symbol "$project" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
          Global symbol "$sample" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
          Global symbol "$lane" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
          Global symbol "$barcode" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
          Global symbol "$reference" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 753.
          syntax error at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 761, near "}"
          /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm has too many errors.
          Compilation failed in require at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
          BEGIN failed--compilation aborted at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment.pm line 61.
          Compilation failed in require at /usr/local/bin/configureBclToFastq.pl line 250.
          BEGIN failed--compilation aborted at /usr/local/bin/configureBclToFastq.pl line 250.

          Comment


          • #6
            As I recollect bcl2fastq requires a specific version of perl (I think 5.12). If you are using other newer versions then it can lead to errors. Make sure when you run bcl2fastq that version is one available.

            Did you do this install from source or by using the package?

            Comment


            • #7
              Is there any reason why you're using such an old version of bcl2fastq? Last year they updated to bcl2fastq 2 and it runs much better. We previously had trouble demultiplexing hiseq runs with the older versions of bcl2fastq but now it's a much better program for that. You can get newer versions at http://support.illumina.com/sequenci...-software.html

              Comment


              • #8
                bcl2fastq v.1.8.4 works fine with most (older) HiSeq.

                Only HiSeq 3K,4K,X and NextSeq require the new bcl2fastq v.2.x series.

                Comment


                • #9
                  Originally posted by GenoMax View Post
                  bcl2fastq v.1.8.4 works fine with most (older) HiSeq.

                  Only HiSeq 3K,4K,X and NextSeq require the new bcl2fastq v.2.x series.
                  We have a 2500 that was upgraded from a 2000 and we ran into issues using 1.8.4 and earlier to demux our runs, whereas 2 worked right out of the gate fairly smoothly for us.

                  I know that certain older versions of RTA may require older bcl2fastq, so I figured maybe that's why he was using that version; otherwise I've been really happy with the improvements in 2.x.

                  Comment


                  • #10
                    Just to clarify bcl2fastq v.2.x is compatible with all sequencers AFAIK.

                    @saupra you may want to give that version a try. Caveat (as mentioned by @moatman) is that you need to use v.1.8.x if following is applicable

                    For Illumina sequencing systems runnings RTA versions earlier than 1.18.54, use bcl2fastq Conversion Software v1.8.4.

                    Comment

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