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  • BFAST - DATA SoLID

    when I run the script solid2fastq with the following command:

    $ bfast-0.6.1c/scripts/solid2fastq n-10000000 reads barcode2/barcode2_F3.csfasta barcode2/barcode2_F3.qual

    Surgi this error message:

    Outputting, currently on:
    0csfasta_name = [> 9_42_916_F3]
    qual_name = [> 9_42_20_F3]
    ************************************************** **********
    In function "fastq_read" Fatal Error [outofrange]. Variable / Value: read-> name! = Qual_name.
    Message: Read names did not match.
    ***** Exiting due to errors *****
    ************************************************** **********

    What would it be?

  • #2
    Originally posted by jeferson View Post
    when I run the script solid2fastq with the following command:

    $ bfast-0.6.1c/scripts/solid2fastq n-10000000 reads barcode2/barcode2_F3.csfasta barcode2/barcode2_F3.qual

    Surgi this error message:

    Outputting, currently on:
    0csfasta_name = [> 9_42_916_F3]
    qual_name = [> 9_42_20_F3]
    ************************************************** **********
    In function "fastq_read" Fatal Error [outofrange]. Variable / Value: read-> name! = Qual_name.
    Message: Read names did not match.
    ***** Exiting due to errors *****
    ************************************************** **********

    What would it be?
    The reads in the CSFASTA should be in the same order as the QUAL file, which is not the case above. Have you manipulated the files prior to using "solid2fastq"? I see that you are barcoding, does that pre-process the CSFASTA/QUAL files?

    Nils

    Comment


    • #3
      Nils:

      This touches on one of my 'hot topics' in error message -- the lack of enough information for the end user to figure out what is exactly wrong. Maybe you can change the program so that it outputs what read names are not matching. That would help in determining what is going wrong. Example:

      Message: Read names did not match: 'read xyz' versus 'readABC'

      Comment


      • #4
        Perhaps like this...?

        Outputting, currently on:
        0csfasta_name = [> 9_42_916_F3]
        qual_name = [> 9_42_20_F3]

        But why not just skip reads if names don't match?

        Comment


        • #5
          Originally posted by westerman View Post
          Nils:

          This touches on one of my 'hot topics' in error message -- the lack of enough information for the end user to figure out what is exactly wrong. Maybe you can change the program so that it outputs what read names are not matching. That would help in determining what is going wrong. Example:

          Message: Read names did not match: 'read xyz' versus 'readABC'
          The error message does describe exactly what is wrong in my opinion. Namely that the read named "> 9_42_916_F3" from the CSFASTA file does not match the read named "> 9_42_20_F3 " in the corresponding QUAL file. I am a bit confused at what more information is required.

          Originally posted by Chipper View Post
          Perhaps like this...?

          Outputting, currently on:
          0csfasta_name = [> 9_42_916_F3]
          qual_name = [> 9_42_20_F3]

          But why not just skip reads if names don't match?
          Since the assumption is that each read in the CSFASTA is present in the QUAL file in the same order. If the files are corrupt etc. then this it is appropriate to abort. I prefer to be conservative in this case.

          Comment


          • #6
            Originally posted by nilshomer View Post
            The error message does describe exactly what is wrong in my opinion. Namely that the read named "> 9_42_916_F3" from the CSFASTA file does not match the read named "> 9_42_20_F3 " in the corresponding QUAL file. I am a bit confused at what more information is required.
            Ah, I read too fast after a several day hiatus from SeqAnswers and was only focusing in on the parts between the stars thinking for some reason that the starred part was the only important information. Probably if I was actually staring at the message on the screen instead of staring at it on a web page then the part of the message that told me the names of the sequences would jump out.

            My apologies Nils. I should have known that you would write useful messages.


            However going back to the original poster -- jeferson -- I wonder why he/she could not figure out what was the cause of the problem? If I were to guess it may because of the use of the term:

            read-> name! = Qual_name

            While the lines above that message talk about

            0csfasta_name and qual_name

            Which might, to some people, not mean the same as 'read' and 'Qual_name'. Furthermore the use of '! =' might not mean, to some people, 'not equal' and even if it means 'not equal' to them it might not come across to them that the two files need to have the same read names in them.

            OTOH, writing error messages so that they are understandable to a wide range of people is difficult. In bioinformatics and especially 2ndgen bioinformatics we should assume that we are dealing with intelligent people who can figure out problems given enough information.

            Anyway, enough rambling. Nils: your error message is fine.

            Comment


            • #7
              Thank you for answering the topic before. run !

              But I have a new problem.
              which the error?

              $bfast-0.6.2a/bfast fasta2brg -f reference/human/hg18.fa
              -bash: bfast-0.6.2a/bfast: not directory

              Comment


              • #8
                sorry. I rolled the problem.

                Comment


                • #9
                  Originally posted by jeferson View Post
                  sorry. I rolled the problem.

                  $bfast-0.6.2a/bfast/bfast fasta2brg -f reference/human/hg18.fa

                  Comment


                  • #10
                    can someone help with this error.

                    $ bfast-0.6.2a/bfast/bfast match -f reference/human/hg18.fa -A 1 -r reads.1.fastq > bfast.matches.file.hg18.1.bmf
                    ************************************************************
                    Checking input parameters supplied by the user ...
                    Validating fastaFileName reference/human/hg18.fa.
                    Validating readsFileName reads.1.fastq.
                    Validating tmpDir path ./.
                    **** Input arguments look good!
                    ************************************************************
                    ************************************************************
                    Printing Program Parameters:
                    programMode: [ExecuteProgram]
                    fastaFileName: reference/human/hg18.fa
                    mainIndexes [Auto-recognizing]
                    secondaryIndexes [Not Using]
                    readsFileName: reads.1.fastq
                    offsets: [Using All]
                    loadAllIndexes: [Not Using]
                    space: [Color Space]
                    startReadNum: 1
                    endReadNum: 2147483647
                    keySize: [Not Using]
                    maxKeyMatches: 8
                    maxNumMatches: 384
                    whichStrand: [Both Strands]
                    numThreads: 1
                    queueLength: 10000
                    tmpDir: ./
                    timing: [Not Using]
                    ************************************************************
                    Searching for main indexes...
                    ************************************************************
                    In function "GetIndexFileNames": Fatal Error[OutOfRange]. Variable/Value: reference/human/hg18.fa.cs.
                    Message: Could not find any indexes with the given prefix.
                    ***** Exiting due to errors *****
                    ************************************************************

                    Comment


                    • #11
                      What are the names of your index files?

                      Comment


                      • #12
                        hg18.fa.cs.2.1.bif

                        Comment


                        • #13
                          Originally posted by jeferson View Post
                          hg18.fa.cs.2.1.bif
                          It looks like you only built index #2: "hg18.fa.cs.2.1.bif". You probably used 'bfast index -i 2' instead of 'bfast index -i 1'. The index #s must be starting at one.

                          Anyhow, did you mean to build ten indexes (as recommended by the manual)? In that case, you must number your index with 'bfast index -i'. I would recommending reading section 7.1 of the BFAST manual.

                          Comment


                          • #14
                            I need help to configure bfast.submit.pl.
                            when I run the command "bfast.submit.pl -man", what appears is the source code.

                            Comment


                            • #15
                              Weird.

                              Create a file with this on it (./file.pl):

                              use Pod::Usage;

                              pod2usage(-exitstatus => 0, -verbose => 2);

                              __END__
                              =head1 SYNOPSIS
                              test
                              And then run:

                              perl ./file.pl
                              What output do yo get?
                              -drd

                              Comment

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