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  • Jetse
    replied
    Did anyone of you solve this problem?
    I have exactly the same problem now.

    Mapping left_kept_reads to genome GRCh37_gatk_colorspace with Bowtie
    Mapping left_kept_reads_seg1 to genome GRCh37_gatk_colorspace with Bowtie (1/2)
    Mapping left_kept_reads_seg2 to genome GRCh37_gatk_colorspace with Bowtie (2/2)
    Mapping right_kept_reads to genome GRCh37_gatk_colorspace with Bowtie
    [FAILED]
    Error running bowtie:
    Too few quality values for read: 28 I
    are you sure this is a FASTQ-int file?
    terminate called after throwing an instance of 'int'

    All 4 files are exactly 200000 lines (so 100000 reads). Mapping the left reads works, but when mapping the right reads it fails...

    [EDIT]
    For anyone who has this error too, check whether you have added the --quals option, also check the command on order of files (first all csfasta files than the qual files). This solved my error...
    Last edited by Jetse; 03-26-2013, 08:02 AM. Reason: solved

    Leave a comment:


  • Chirag
    replied
    Hey guys,
    How did you solve this problem ? Could you please help me with this ?
    I am also getting this error, when using tophat mapping on colorspace file.

    This is my command: [Works fine until half-way]

    tophat --output-dir /results --color -p 8 --no-coverage-search /bowtie_alignment_reference/mm9_c F3.csfasta F3.QV.qual


    I get this error:
    Mapping left_kept_reads_seg1 to genome mm9_c with Bowtie (1/3)
    Mapping left_kept_reads_seg2 to genome mm9_c with Bowtie (2/3)
    Mapping left_kept_reads_seg3 to genome mm9_c with Bowtie (3/3)

    [2012-10-20 22:11:02] Mapping right_kept_reads to genome mm9_c with Bowtie
    [FAILED]
    Error running bowtie:
    Too few quality values for read: 39 I
    are you sure this is a FASTQ-int file?
    terminate called after throwing an instance of 'int'


    regards
    Chirag

    Leave a comment:


  • adamdeluca
    replied
    Truncated Qual file

    I have had this error when SAET failed and a truncated qual file was produced.

    Leave a comment:


  • wangleibio
    replied
    ok,i have deleted it, thanks!

    Leave a comment:


  • nilshomer
    replied
    Please only post to one forum. Cross-posting is like spam, unacceptable.

    Leave a comment:


  • question about Solid data analysis using bowtie?


    hello ,everyone
    I am trying to run bowtie with the solid sequence data flower9_1_F3.csfasta and flower9_1_F3_QV.qual
    I built the bowtie-build -C index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run the command:
    bowtie -n 3 --best --strata -a -e 150 -p 4 ../cDNA_reference/TAIR9_cdna -C -f flower9_1_F3.csfasta -Q flower9_1_F3_QV.qual --un fllower9-unmap > flower9-map &
    and the output i got is an error showing on console

    [wanglei@mu01 data]$ [wanglei@mu01 data]$ Too few quality values for read: 425_2031_2008_F3
    are you sure this is a FASTQ-int file?
    terminate called after throwing an instance of 'int'
    Too few quality values for read: 425_2042_1847_F3
    are you sure this is a FASTQ-int file?
    terminate called after throwing an instance of 'int'
    Too few quality values for read: 1277_2042_2013_F3
    are you sure this is a FASTQ-int file?
    Could you please help me to sort out this issue?
    thanks
    wanglei

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