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  • Velvet Columbus (No roadmap)

    Hi, I have been running velveth and velvetg for mapping on a reference file (Columbus extension) but I am getting the following error:

    First I ran velveth, using the following script:
    ./velveth directory 21 -reference Concatenated.fasta -shortPaired -sam Bowtie2_sorted.sam

    And the directory result was:

    total 249760
    drwxr-xr-x 2 vramirezc ucb 4096 Apr 24 11:26 ./
    drwxr-xr-x 122 vramirezc ucb 12288 Apr 24 11:26 ../
    -rw-r--r-- 1 vramirezc ucb 1158 Apr 24 11:53 Log
    -rw-r--r-- 1 vramirezc ucb 255727679 Apr 24 11:26 Sequences

    Later, I ran velvetg using:
    ./velvetg directory -ins_length 400 -exp_cov 10 -min_contig_lgth 100 -unused_reads yes

    And then I just obtained an O file (the error file was empty) saying:
    [0.000001] No Roadmap file to build upon! Please run velveth (see manual)
    [0.000000] No Roadmap file to build upon! Please run velveth (see manual)
    [0.000000] No Roadmap file to build upon! Please run velveth (see manual)
    [0.000000] No Roadmap file to build upon! Please run velveth (see manual)

    Clearly there is no roadmap in the directory file, but I do not know why. Could you please help me?

  • #2
    Solved!

    The problem was solved*just by recompiling the program using make 'LONGSEQUENCES=Y' (for some reason using make 'LONGSEQUENCES=1' did not work). It seems like the reference file was too long.*

    Comment

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