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
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
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