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  • SOAPddenovo v1.05 error-Cannot open output_prefix.kmerFreq.

    Hello,

    We are using SOAPdenovov1.05 on paired end 36bp Illumina reads with this command:
    [s0977659@ris-lx03 bin]$ ./SOAPdenovo-31mer all -p 4 -s /LBEP/Laura/JUNE_2012/14_june_2012/SOAPdenovo_140612/Inputs/AB10.config -o AB10

    The Error I get is:
    Cannot open AB10.kmerFreq. Now exit to system...

    Prior to this output looks ok:
    Version 1.05: released on July 29th, 2010

    pregraph -s /LBEP/Laura/JUNE_2012/14_june_2012/SOAPdenovo_140612/Inputs/AB10b.config -p 4 -o AB10
    In /LBEP/Laura/JUNE_2012/14_june_2012/SOAPdenovo_140612/Inputs/AB10b.config, 1 libs, max seq len 100, max name len 256

    4 thread created
    read from file:
    /LBEP/Laura/Genome_assemblies/ILLUMINARUN3/concat_files/correct_heads/Paired_Filtered_2012-05-18/3_2008/3_2008_1.fq
    read from file:
    /LBEP/Laura/Genome_assemblies/ILLUMINARUN3/concat_files/correct_heads/Paired_Filtered_2012-05-18/3_2008/3_2008_2.fq
    time spent on hash reads: 6s, 1827824 reads processed
    [LIB] 0, avg_ins 500, reverse 0
    3017193 nodes allocated, 20004683 kmer in reads, 20004683 kmer processed
    2924786 linear nodes


    Config file is:
    #maximal read length
    # Lines start with '#' are ignored by the assembler
    max_rd_len=100
    [LIB]
    #average insert size
    avg_ins=500
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=3
    #in which order the reads are used while scaffolding
    rank=1
    #fastq file for read 1
    q1=/path/to/3_2008_1.fq
    #fastq file for read 2 always follows fastq file for read 1
    q2=/path/to/3_2008_2.fq
    #fastq file for single reads
    #q=/path/to/3_2008_single.fq

    #87 scaffolds from 2858 contigs sum up 2802411bp, with average length 32211, 1 gaps filled
    #188 scaffolds&singleton sum up 2881315bp, with average length 15326
    #the longest is 233637bp,scaffold N50 is 65253 bp, scaffold N90 is 19282 bp

    I am new to SOAPdenvo, but has anyone had similar problems?

    Thanks,

    Laura

  • #2
    You don't have admin rights or something

    Hi Laura

    I actually had this same problem today!
    It's because I did not have administrator's rights to the folder that I wanted to save my output (-o) file in!
    As soon as I changed my output file location, and tried again, the run worked just fine.

    Hope this helps!
    Have fun

    Comment

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