SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SVDetect : unable to get links.filtered.unique.defined tarunmishra.rsg Bioinformatics 2 10-10-2012 09:02 AM
PubMed: [Cancer genome defined by the next generation sequencers]. Newsbot! Literature Watch 0 12-17-2011 02:10 AM
PubMed: A novel and well-defined benchmarking method for second generation read mappi Newsbot! Literature Watch 0 09-20-2011 02:00 AM
BAM : select only alignment of a defined length NicoBxl Bioinformatics 0 08-18-2011 03:29 AM
PubMed: A ChIP-seq defined genome-wide map of vitamin D receptor binding: Association Newsbot! Literature Watch 0 08-26-2010 02:00 AM

Reply
 
Thread Tools
Old 11-15-2010, 11:28 PM   #1
Gangcai
Member
 
Location: Shanghai, China

Join Date: Nov 2009
Posts: 30
Default 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
Gangcai is offline   Reply With Quote
Old 11-16-2010, 01:39 AM   #2
Gangcai
Member
 
Location: Shanghai, China

Join Date: Nov 2009
Posts: 30
Default

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."
Gangcai is offline   Reply With Quote
Old 11-16-2010, 09:26 PM   #3
Gangcai
Member
 
Location: Shanghai, China

Join Date: Nov 2009
Posts: 30
Default

I have fixed the preprocessing step, but "'original_BS' is not defined" error still exist...
Gangcai is offline   Reply With Quote
Reply

Tags
alignment, bisulfite, mapping, rrbs

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO