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  • BS_Seeker 'original_BS' is not defined

    Hi everybody,
    I am using BS_Seeker(http://pellegrini.mcdb.ucla.edu/BS_S...BS_Seeker.html ) to process the bisulfite converted sequencing data.
    There is no trouble for genome preprocessing steps(Preprocessing_genome.py), but there is error when running BS_Seeker.py:

    part of the code:
    python BS_Seeker.py -i $fastq_file -t N -e 50 -p $bowtie -m 3 -d $ref_genome -o $outfile

    error:
    ....
    ...
    ref seq: 0025 ( 27682 bp)
    ref seq: 0029 ( 590426 bp)
    ref seq: 0092 ( 155270560 bp)
    ref seq: 0090 ( 39786 bp)
    # 93 ref sequence(s)
    # 3340425 BS reads
    Traceback (most recent call last):
    File "/picb/compbio3/gangcai/project/RRBS/scripts/BS_SEEKER/BS_Seeker.py", line 905, in ?
    logoutf.write("# %d raw BS-reads ( %d bp)"%(len(original_bs_reads),len(original_BS))+"\n")
    NameError: name 'original_BS' is not defined

  • #2
    I have re-checked the reference preprocessing, there is one error I missed:
    "Could not allocate space for a joined string of 2897310462 elements.
    Switching to a packed string representation."

    Comment


    • #3
      I have fixed the preprocessing step, but "'original_BS' is not defined" error still exist...

      Comment

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