Bowtie-build incomplete

2012-02-09
2013-06-05
  • Nobody/Anonymous

    I was trying to build 3 new bowtie indexes with Macaca mulatta alone and
    > with SIV isolates 239 and E543. The only files that were built were the 3
    > and 4.ebwt files. I also received an error about the size of the reference
    > sequence. We tried to build the index using the original unzipped fasta chromosome
    > files and managed to get through 1-4.ebwt but stopped the program before
    > allowing it to finish because we assumed it was working. When we tried to go
    > back and use the same fasta files saved under a shorter name (chr1, chr2
    > etc) we ran into the problem of only getting the 3 and 4 index files. The
    > same happened when we tried to use a combined chromosome fasta file. I am
    > including text from Terminal below. Any advice? Any chance you already have
    > this index available?
    >
    > -Claire
    >
    > mac6:bowtie-0.12.7 mac6$ bowtie-build
    > /Users/mac6/Documents/NGS_Clients/Nick_Maness/Illumina_data/Genomes/Rhesus_genome/Edited_fasta_files/Macaca_mulatta_combined_chromosome_fasta_file/mmul_chromosomes.fa
    > mmul
    > Settings:
    >   Output files: "mmul.*.ebwt"
    >   Line rate: 6 (line is 64 bytes)
    >   Lines per side: 1 (side is 64 bytes)
    >   Offset rate: 5 (one in 32)
    >   FTable chars: 10
    >   Strings: unpacked
    >   Max bucket size: default
    >   Max bucket size, sqrt multiplier: default
    >   Max bucket size, len divisor: 4
    >   Difference-cover sample period: 1024
    >   Endianness: little
    >   Actual local endianness: little
    >   Sanity checking: disabled
    >   Assertions: disabled
    >   Random seed: 0
    >   Sizeofs: void*:8, int:4, long:8, size_t:8
    > Input files DNA, FASTA:
    >
    > /Users/mac6/Documents/NGS_Clients/Nick_Maness/Illumina_data/Genomes/Rhesus_genome/Edited_fasta_files/Macaca_mulatta_combined_chromosome_fasta_file/mmul_chromosomes.fa
    > Reading reference sizes
    > Error: Reference sequence has more than 2^32-1 characters!  Please divide
    > the
    > reference into batches or chunks of about 3.6 billion characters or less
    > each
    > and index each independently.
    >   Time reading reference sizes: 00:00:58
    > Total time for call to driver() for forward index: 00:00:58
    > Command: bowtie-build
    > /Users/mac6/Documents/NGS_Clients/Nick_Maness/Illumina_data/Genomes/Rhesus_genome/Edited_fasta_files/Macaca_mulatta_combined_chromosome_fasta_file/mmul_chromosomes.fa
    > mmul

     
  • Nobody/Anonymous

    Great delivery. Great arguments. Keep up the good work.
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