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  • Abyss-PE error

    Hello
    I am newer for abyss-pe assembler tool, the following mention below error is occur, but in my data there is no any duplicate ID present and i also run on different k-mer values are 32, 64,76.
    The command I used is: abyss-pe name=de_novo_assemble k=76 in='D2_R1_split_filter.fastq D2_R2_split_filter.fastq'

    Please guide me to solve this error.

    genomics2@genomics2-Precision-Tower-7810:~/tools/imrdenom-0.4.1/abyss$ abyss-pe name=de_novo_assemble k=76 in='D2_R1_split_filter.fastq D2_R2_split_filter.fastq'
    ABYSS -k76 -q3 --coverage-hist=coverage.hist -s de_novo_assemble-bubbles.fa -o de_novo_assemble-1.fa D2_R1_split_filter.fastq D2_R2_split_filter.fastq
    ABySS 2.0.2
    ABYSS -k76 -q3 --coverage-hist=coverage.hist -s de_novo_assemble-bubbles.fa -o de_novo_assemble-1.fa D2_R1_split_filter.fastq D2_R2_split_filter.fastq
    Reading `D2_R1_split_filter.fastq'...
    `D2_R1_split_filter.fastq': discarded 36 reads containing non-ACGT characters
    Reading `D2_R2_split_filter.fastq'...
    `D2_R2_split_filter.fastq': discarded 308 reads containing non-ACGT characters
    Loaded 499505416 k-mer
    Minimum k-mer coverage is 85
    Using a coverage threshold of 3...
    The median k-mer coverage is 7
    The reconstruction is 128007680
    The k-mer coverage threshold is 2.64575
    Setting parameter e (erode) to 3
    Setting parameter E (erodeStrand) to 1
    Setting parameter c (coverage) to 2.64575
    Generating adjacency
    Added 1000899508 edges.
    Eroding tips
    Eroded 346910042 tips.
    Eroded 0 tips.
    Pruning tips shorter than 1 bp...
    Pruned 12919 k-mer in 12919 tips.
    Pruning tips shorter than 2 bp...
    Pruned 7306 k-mer in 4035 tips.
    Pruning tips shorter than 4 bp...
    Pruned 12877 k-mer in 4525 tips.
    Pruning tips shorter than 8 bp...
    Pruned 34042 k-mer in 6708 tips.
    Pruning tips shorter than 16 bp...
    Pruned 122994 k-mer in 12951 tips.
    Pruning tips shorter than 32 bp...
    Pruned 406365 k-mer in 23260 tips.
    Pruning tips shorter than 64 bp...
    Pruned 1190519 k-mer in 37110 tips.
    Pruning tips shorter than 76 bp...
    Pruned 511513 k-mer in 11648 tips.
    Pruning tips shorter than 76 bp...
    Pruned 1247 k-mer in 29 tips.
    Pruning tips shorter than 76 bp...
    Pruned 113185 tips in 9 rounds.
    Marked 3654131 edges of 1653207 ambiguous vertices.
    Removing low-coverage contigs (mean k-mer coverage < 2.64575)
    Found 150295213 k-mer in 2085178 contigs before removing low-coverage contigs.
    Removed 25438641 k-mer in 702810 low-coverage contigs.
    Split 1403295 ambigiuous branches.
    Eroding tips
    Eroded 2885197 tips.
    Eroded 0 tips.
    Pruning tips shorter than 1 bp...
    Pruned 8520 k-mer in 8520 tips.
    Pruning tips shorter than 2 bp...
    Pruned 4180 k-mer in 2248 tips.
    Pruning tips shorter than 4 bp...
    Pruned 5448 k-mer in 1879 tips.
    Pruning tips shorter than 8 bp...
    Pruned 9936 k-mer in 2001 tips.
    Pruning tips shorter than 16 bp...
    Pruned 25514 k-mer in 2518 tips.
    Pruning tips shorter than 32 bp...
    Pruned 64040 k-mer in 3164 tips.
    Pruning tips shorter than 64 bp...
    Pruned 163941 k-mer in 3939 tips.
    Pruning tips shorter than 76 bp...
    Pruned 75415 k-mer in 1181 tips.
    Pruning tips shorter than 76 bp...
    Pruned 104 k-mer in 8 tips.
    Pruning tips shorter than 76 bp...
    Pruned 25458 tips in 9 rounds.
    Popping bubbles
    Removed 9468 bubbles.
    Removed 9468 bubbles
    Marked 911690 edges of 418182 ambiguous vertices.
    Left 4725 unassembled k-mer in circular contigs.
    Assembled 120784058 k-mer in 552479 contigs.
    Removed 377890760 k-mer.
    The signal-to-noise ratio (SNR) is -4.9238 dB.
    AdjList -k76 -m50 --dot de_novo_assemble-1.fa >de_novo_assemble-1.dot
    abyss-filtergraph --dot -k76 -g de_novo_assemble-2.dot1 de_novo_assemble-1.dot de_novo_assemble-1.fa >de_novo_assemble-1.path
    MergeContigs -k76 -g de_novo_assemble-2.dot -o de_novo_assemble-2.fa de_novo_assemble-1.fa de_novo_assemble-2.dot1 de_novo_assemble-1.path
    PopBubbles --dot -j2 -k76 -p0.9 -g de_novo_assemble-3.dot de_novo_assemble-2.fa de_novo_assemble-2.dot >de_novo_assemble-2.path
    MergeContigs -k76 -o de_novo_assemble-3.fa de_novo_assemble-2.fa de_novo_assemble-2.dot de_novo_assemble-2.path
    The minimum coverage of single-end contigs is 2.5625.
    The minimum coverage of merged contigs is 2.64706.
    Consider increasing the coverage threshold parameter, c, to 2.64706.
    awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \
    de_novo_assemble-2.path de_novo_assemble-1.fa >de_novo_assemble-indel.fa
    ln -sf de_novo_assemble-3.fa de_novo_assemble-unitigs.fa
    abyss-map -j2 -l40 D2_R1_split_filter.fastq D2_R2_split_filter.fastq de_novo_assemble-3.fa \
    |abyss-fixmate -l40 -h de_novo_assemble-3.hist \
    |sort -snk3 -k4 \
    |DistanceEst -j2 -k76 -l40 -s1000 -n10 -o de_novo_assemble-3.dist de_novo_assemble-3.hist
    Building the suffix array...
    Building the Burrows-Wheeler transform...
    Building the character occurrence table...
    error: duplicate read ID `NS500278:15:H2LTCAFXX:1:11101:12362:1019/1'
    error: `de_novo_assemble-3.hist': No such file or directory
    /usr/local/bin/abyss-pe:559: recipe for target 'de_novo_assemble-3.dist' failed
    make: *** [de_novo_assemble-3.dist] Error 1
    make: *** Deleting file 'de_novo_assemble-3.dist'



    Thank you,
    Divya

  • #2
    @divya: Please don't post new questions in unrelated threads. You are not likely to get answers if you do that. I moved your post to a new question.

    For future reference to create a new thread do this: From seqanswers.com --> Forum (link at top left of page) --> Select forum you want to post in --> Click on "New Thread" button at top left of next page.

    Comment


    • #3
      Have you checked your file with grep to see if you indeed have two records?

      Code:
      $ grep "NS500278:15:H2LTCAFXX:1:11101:12362:1019/1" D2_R1_split_filter.fastq

      Comment


      • #4
        sir,
        I have already checked with this grep command , there are no duplicates reads both in R1 and R2 files.
        Last edited by divya; 01-12-2017, 08:59 PM.

        Comment

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