Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • bcl2fastq run error

    vanessa@vanessa:~$ /usr/local/bin/configureBclToFastq.pl --input-dir /media/vanessa/UUI/ngs/Data/Intensities/BaseCalls --output-dir /media/vanessa/UUI Unaligned --sample-sheet /media/vanessa/UUI/ngs/Data/Intensities/BaseCalls/SampleSheet.csv
    "my" variable $value masks earlier declaration in same statement at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 760.
    syntax error at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 747, near "$variable qw(ELAND_FASTQ_FILES_PER_PROCESS)"
    Global symbol "$variable" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 749.
    syntax error at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 751, near "$directory qw(ELAND_GENOME)"
    Global symbol "$self" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$directory" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$project" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$sample" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$lane" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$barcode" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 753.
    Global symbol "$reference" requires explicit package name at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 753.
    syntax error at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm line 761, near "}"
    /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment/Config.pm has too many errors.
    Compilation failed in require at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment.pm line 61.
    BEGIN failed--compilation aborted at /usr/local/lib/bcl2fastq-1.8.3/perl/Casava/Alignment.pm line 61.
    Compilation failed in require at /usr/local/bin/configureBclToFastq.pl line 239.
    BEGIN failed--compilation aborted at /usr/local/bin/configureBclToFastq.pl line 239.

    can any body solve this errors

  • #2
    Is there a space in the --output-dir declaration "/vanessa/UUI Unaligned"?

    Comment


    • #3
      @ Genomax

      Yes ther is space ,

      vanessa@vanessa:~$ /usr/local/bin/configureBclToFastq.pl --input-dir /media/vanessa/UUI/ngs/Data/Intensities/BaseCalls --output-dir /media/vanessa/UUI/ Unaligned --sample-sheet /media/vanessa/UUI/ngs/Data/Intensities/BaseCalls/SampleSheet.csv

      Please watch the screen shot of usr/local/bin

      is there any other requirements other than existed ,like simple XML executables , to begin ?
      Attached Files

      Comment


      • #4
        When you specify an --output-dir location the "Unaligned" directory is automatically created by the configureBclToFastq.pl script in that directory. You do not need to specify it on the command line.

        Omit the "Unaligned" from your command line and the program should work.

        You may want to consider adding "--fastq-cluster-count 0" (without quotes) to your command line if you want the sequence output in a single file as opposed to 4 millon fastq sequences each in more than one file.

        Comment


        • #5
          solved

          I solved it , Thanks buddy

          Comment


          • #6
            @ Genomax

            Thanks for the above guidelines
            Finally I could able to run the Bcl2fastq , i tried to demultiplex 2X100 pe nextra exome data with 8 bp indices ,unfortunately all fastq files were moved to undetermined_Indices folder , in which sample_lane1 , sample_lane2 has no data except sample sheet ,rest of the folders lane 3 to lane 8 goy sample sheet + fasq.gz files

            the command I uses is /usr/local/bin/configureBclToFastq.pl --input-dir
            <BaseCalls_dir> --output-dir <Unaligned> --sample-sheet
            <BaseCalls_dir>/SampleSheet.csv --use-bases-mask y100n,I8n,Y100N
            Last edited by wintergreen36; 08-05-2014, 12:21 AM. Reason: missing content

            Comment


            • #7
              If lanes 3-8 worked fine then the format of your sample sheet as well as the command line is fine. Did you look at the Demultiplex_Stats.htm file to ascertain that the demultiplexing had worked as expected (i.e. more reads assigned to samples than are in the "undetermined" pool)? Is the situation reverse for lanes 1 and2 (i.e more reads in undetermined row for lanes 1/2)?

              Start looking at the fastq ID headers of the "lane1_undetermined*" files to see if there are any problems with the tag reads (i.e. N's etc).

              Comment


              • #8
                Hello GEnomax thanks for ur support I SUCCESFULY INSTALLED bcl2fastq BUt while running a project i got the follwing error ,

                [2014-08-12 13:23:41] [vanessa] [Temp/L006_R1_demux_summary.xml] Processing BCL files for lane 6, tile 2316, read 1
                [2014-08-12 13:24:14] [vanessa] [Temp/L006_R1_demux_summary.xml] runtime error: boost::filesystem::rename: No such file or directory: "/media/vanessa/Sandor_1/Unaligned/Undetermined_indices/Sample_lane6/lane6_Undetermined_L006_R1_001.fastq.tmp.gz", "/media/vanessa/Sandor_1/Unaligned/Undetermined_indices/Sample_lane6/lane6_Undetermined_L006_R1_001.fastq.gz"
                make: *** [Temp/L006_R1_demux_summary.xml] Error 2

                Could you please guide me how to over come this error

                thanks

                Comment


                • #9
                  Unfortunately not enough information (at least for me) in that error snippet. Have you looked further up in the log file to see if there was any other errors (missing BCL/stat files etc)? Were there any notes from the facility that ran the flowcell about lane 6 experiencing problems during run (no clusters may be a possibility if the error above is real)?

                  Comment


                  • #10
                    I ran this there was no errors during the run

                    Comment


                    • #11
                      Have you tried removing entries for lane 6 samples from your samplesheet and checking to see if the remaining lanes demultiplex?

                      Comment


                      • #12
                        I haven't , There was no boost libs installed in my system , I just updated libboost all ; started run again

                        Comment


                        • #13
                          What was the impact of these boost lib on Bcl2fastq run?

                          Comment


                          • #14
                            There was no boost lib in my system , what's the impact of boost lib on bcl2fastq run ? I just installed lib boost and started the bcl2fastq run again.

                            Comment


                            • #15
                              That is odd. You have been able to run bcl2fastq before and I would have though that Boost libraries are required for the software to function. Let us see what happens with the new run.

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Recent Developments in Metagenomics
                                by seqadmin





                                Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
                                09-23-2024, 06:35 AM
                              • seqadmin
                                Understanding Genetic Influence on Infectious Disease
                                by seqadmin




                                During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.

                                Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...
                                09-09-2024, 10:59 AM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, 10-02-2024, 04:51 AM
                              0 responses
                              11 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 10-01-2024, 07:10 AM
                              0 responses
                              19 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 09-30-2024, 08:33 AM
                              0 responses
                              24 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 09-26-2024, 12:57 PM
                              0 responses
                              17 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X