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  • abyss-pe - no LIB-contigs.fa !!!

    Hi all,

    I'm new at using ABySS and when I ran the following command on ABySS v 1.2.7:

    abyss-pe k=25 n=10 in=' /path/to/reads/file/1 /path/to/read/files/2' name=LIB

    the following files got created in the output directory:
    coverage.hist LIB-1.adj LIB-1.fa LIB-1.path LIB-3.adj LIB-3.fa LIB-3.sam.gz LIB-bubbles.fa LIB-indel.fa

    Now, obviously I'm missing something because the main assembly file, LIB-contigs.fa is missing! Any ideas what I'm doing wrong?

    Any help much appreciated! Thanks in advance!
    Last edited by savkart; 07-30-2011, 05:40 AM.

  • #2
    Did you check if it completed? if yes, what was the error?

    Comment


    • #3
      I'm a new ABySS user, too. What is the best way to tell if the whole abyss-pe program has completed? If there is no error message can I assume all of the separate pieces ran properly? What is the last file that gets made from an abyss-pe run?

      Comment


      • #4
        Originally posted by kweitemier View Post
        I'm a new ABySS user, too. What is the best way to tell if the whole abyss-pe program has completed? If there is no error message can I assume all of the separate pieces ran properly? What is the last file that gets made from an abyss-pe run?
        prefix.contigs.fa

        Comment


        • #5
          i have similar problem with abyss-pe

          contig.fa file not created?

          KAligner: Aligner.cpp:201: void Aligner<SeqPosHashMap>::coalesceAlignments(const std::string&, const std::string&, const std::map<unsigned int, std::vector<Alignment, std::allocator<Alignment> >, std::less<unsigned int>, std::allocator<std:air<const unsigned int, std::vector<Alignment, std::allocator<Alignment> > > > >&, oiterator&) [with oiterator = affix_ostream_iterator<Alignment, char, std::char_traits<char> >, SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer, std::equal_to<Kmer>, google::libc_allocator_with_realloc<std:air<const Kmer, Position> > >]: Assertion `qstep >= 0 && qstep <= m_hashSize' failed.


          any suggestions?

          Comment


          • #6
            Originally posted by gpcr View Post
            contig.fa file not created?

            KAligner: Aligner.cpp:201: void Aligner<SeqPosHashMap>::coalesceAlignments(const std::string&, const std::string&, const std::map<unsigned int, std::vector<Alignment, std::allocator<Alignment> >, std::less<unsigned int>, std::allocator<std:air<const unsigned int, std::vector<Alignment, std::allocator<Alignment> > > > >&, oiterator&) [with oiterator = affix_ostream_iterator<Alignment, char, std::char_traits<char> >, SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer, std::equal_to<Kmer>, google::libc_allocator_with_realloc<std:air<const Kmer, Position> > >]: Assertion `qstep >= 0 && qstep <= m_hashSize' failed.


            any suggestions?
            1) Check and make sure your FASTA/Q is properly formatted.
            2) What OS and version of ABySS are you running?

            Comment


            • #7
              abyss 1.3.0

              working on linux 64bit with
              using fastq files as input:

              abyss-pe k=25 n=5 in='read_1.fq read_2.fq' name=test_assembly

              Comment


              • #8
                abyss-pe log file

                abyss-pe k=25 n=5 in='read_1.fq read_2.fq' name=l3.assemb
                ABYSS -k25 -q3 --coverage-hist=coverage.hist -s l3.assemb-bubbles.fa -o l3.assemb-1.fa read_1.fq read_2.fq
                ABySS 1.3.0
                ABYSS -k25 -q3 --coverage-hist=coverage.hist -s l3.assemb-bubbles.fa -o l3.assemb-1.fa read_1.fq read_2.fq
                Reading `read_1.fq'
                warning: discarded 182472 reads shorter than 25 bases
                warning: discarded 1432 reads containing non-ACGT characters
                Reading `read_2.fq'
                warning: discarded 238597 reads shorter than 25 bases
                warning: discarded 2700 reads containing non-ACGT characters
                Loaded 146346864 k-mer
                Minimum k-mer coverage is 109
                Using a coverage threshold of 1...
                The median k-mer coverage is 1
                The reconstruction is 146346864
                The k-mer coverage threshold is 1
                Setting parameter e (erode) to 2
                Setting parameter E (erodeStrand) to 0
                Setting parameter c (coverage) to 2
                Generating adjacency
                Generated 296878979 edges
                Eroding tips
                Eroded 90751073 tips
                Eroded 0 tips
                Trimming short branches: 1
                Trimmed 27669 k-mer in 27669 branches
                Trimming short branches: 2
                Trimmed 49179 k-mer in 36794 branches
                Trimming short branches: 4
                Trimmed 111726 k-mer in 49654 branches
                Trimming short branches: 8
                Trimmed 364902 k-mer in 92156 branches
                Trimming short branches: 16
                Trimmed 1014622 k-mer in 137128 branches
                Trimming short branches: 25
                Trimmed 1461718 k-mer in 118076 branches
                Trimming short branches: 25
                Trimmed 2656 k-mer in 368 branches
                Trimming short branches: 25
                Trimmed 28 k-mer in 2 branches
                Trimming short branches: 25
                Trimmed 461847 branches in 8 rounds
                Marked 10864648 edges of 4561491 ambiguous vertices.
                Removing low-coverage contigs (mean k-mer coverage < 2)
                Found 52488076 k-mer in 4455293 contigs before removing low-coverage contigs
                Removed 18572627 k-mer in 1116544 low-coverage contigs
                Split 2149168 ambiguous branches
                Eroding tips
                Eroded 23353 tips
                Eroded 0 tips
                Trimming short branches: 1
                Trimmed 48815 k-mer in 48815 branches
                Trimming short branches: 2
                Trimmed 56035 k-mer in 37425 branches
                Trimming short branches: 4
                Trimmed 116454 k-mer in 46787 branches
                Trimming short branches: 8
                Trimmed 198753 k-mer in 44809 branches
                Trimming short branches: 16
                Trimmed 305805 k-mer in 36891 branches
                Trimming short branches: 25
                Trimmed 275715 k-mer in 19293 branches
                Trimming short branches: 25
                Trimmed 836 k-mer in 97 branches
                Trimming short branches: 25
                Trimmed 14 k-mer in 1 branches
                Trimming short branches: 25
                Trimmed 234118 branches in 8 rounds
                Popping bubbles
                Removed 6309 bubbles
                Removed 6309 bubbles
                Marked 5519489 edges of 2275426 ambiguous vertices.
                108618 unassembled k-mer in circular contigs
                Assembled 32672488 k-mer in 2249263 contigs
                Removed 113381980 k-mer.
                The signal-to-noise ratio (SNR) is -5.36492 dB.
                AdjList -k25 -m30 l3.assemb-1.fa >l3.assemb-1.adj
                PopBubbles -j2 -k25 -p0.9 -g l3.assemb-3.adj l3.assemb-1.fa l3.assemb-1.adj >l3.assemb-1.path
                MergeContigs -k25 -o l3.assemb-3.fa l3.assemb-1.fa l3.assemb-1.adj l3.assemb-1.path
                The minimum coverage of single-end contigs is 2.
                The minimum coverage of merged contigs is 2.
                awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \
                l3.assemb-1.path l3.assemb-1.fa >l3.assemb-indel.fa
                KAligner -j2 -k25 read_1.fq read_2.fq l3.assemb-3.fa \
                |ParseAligns -k25 -h l3.assemb-3.hist \
                |sort -snk3 -k4 \
                |gzip >l3.assemb-3.sam.gz
                KAligner: Aligner.cpp:201: void Aligner<SeqPosHashMap>::coalesceAlignments(const std::string&, const std::string&, const std::map<unsigned int, std::vector<Alignment, std::allocator<Alignment> >, std::less<unsigned int>, std::allocator<std:air<const unsigned int, std::vector<Alignment, std::allocator<Alignment> > > > >&, oiterator&) [with oiterator = affix_ostream_iterator<Alignment, char, std::char_traits<char> >, SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer, std::equal_to<Kmer>, google::libc_allocator_with_realloc<std:air<const Kmer, Position> > >]: Assertion `qstep >= 0 && qstep <= m_hashSize' failed.
                Mateless 0
                Unaligned 1 2.86%
                Singleton 3 8.57%
                FR 5 14.3%
                RF 0
                FF 0
                Different 2 5.71%
                Multimap 0
                Split 24 68.6%
                Total 35
                /bin/bash: line 3: 19667 Aborted KAligner -j2 -k25 read_1.fq read_2.fq l3.assemb-3.fa
                19668 Done | ParseAligns -k25 -h l3.assemb-3.hist
                19669 Done | sort -snk3 -k4
                19670 Done | gzip > l3.assemb-3.sam.gz
                make: *** [l3.assemb-3.hist] Error 134
                make: *** Deleting file `l3.assemb-3.hist'


                Any suggestions?

                Comment


                • #9
                  This the command i use: nohup /usr/local/bin/abyss/bin/abyss-pe k=25 j=8 n=10 in='s_4_1_sequence.txt s_4_2_sequence.txt' name=QC_10

                  Ubuntu 10.04 64 bit, abyss 1.2.5

                  ...at this point try switching to 1.2.5

                  Comment


                  • #10
                    I did essentially the same thing as gpcr, also using abyss 1.3.0, and got the same error message (at the KAligner step). I preceded abyss-pe with nohup, but the result was the same.

                    I tried using an earlier version (1.2.7 happened to be available). With that, I got an error message at the PopBubbles step (just before KAligner):

                    /usr/global/bioscope/bioscope/lib/local/libgomp.so.1: version `GOMP_2.0' not found (required by PopBubbles)

                    Perhaps installing Abyss 1.3.0 updated bioscope so that 1.2.7 would no longer work?

                    Uninstalling 1.3.0 is not a practical option.

                    Thanks.

                    Comment


                    • #11
                      I want to use abyss for paired reads assembly. But I have paired reads (Forward and reverse) in single file. This is the file generated after quality trimming.
                      The file structure is
                      >001_forward
                      ATGC.......
                      >001_reverse
                      ATGC....
                      >002_forward
                      ATGC....
                      >002_reverse
                      ATGC....

                      How do I run Abyss for such file? I need command for this. Any suggestions?

                      Comment

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