Methratio.py ERROR

[lwhitmore]

I am trying to use methratio to analyze methylation sequencing data. Currently I am getting the following error when I run

$ python methratio.py ref=/home/yelab/leanne/Genomes/Human/hg19.fa --out=methratio.txt $HOME/Projects/MethylStudy/BisulfSeq/lung/SRR1045636.sam

Error
Traceback (most recent call last):
File "methratio.py", line 25, in ?
if any(options.chroms): options.chroms = options.chroms.split(',')
NameError: name 'any' is not defined



When i try this command
$ python methratio.py ref=/home/yelab/leanne/Genomes/Human/hg19.fa --out=methratio.txt -s $HOME/Projects/MethylStudy/BisulfSeq/lung/SRR1045636.sam

I get the following error error: Require at least one BSMAP_MAPPING_FILE.
even though I have provided a mapping file

Any help would be greatly appreciated!!

Thanks Leanne

[dpryan]

"-s" is the path to samtools (if it's not already in your path). Just remove that, since your alignment file is not going to be the that (and if it were, you wouldn't have input an alignment file, which is why you got that error).

[maubp]

Which version of Python do you have? The 'any' function was added back in Python 2.5, http://docs.python.org/2.7/library/functions.html#any

[lwhitmore]

So i figured out that the python version was not up to date and so I updated to python 2.6.6 which seemed to fix the initial error

I then ran it and got the following error
@ Thu Mar 20 19:36:43 2014: reading reference /home/yelab/leanne/Genomes/Human/hg19.fa ...
@ Fri Mar 21 01:02:40 2014: reading bsmap_SRR1045636.sam ...
Traceback (most recent call last):
File "/home/yelab/leanne/bin/methratio.py", line 120, in <module>
if infile[-4:].upper() == '.SAM': sam_format, fin = True, os.popen('%ssamtools view -XS %s' % (options.sam_path, infile))
OSError: [Errno 12] Cannot allocate memory

Any Ideas?

Thanks so much
Leanne

[maubp]

It ran out of memory (RAM). How much RAM does this machine have?

[lwhitmore]

24Gbs of RAM

[dpryan]

It takes almost 24 gigs to read in the genome itself (using that script, at least) and that's before the methylation calls, so you'll need a bigger machine or a different tool. The authors should have implemented it differently...

[lwhitmore]

ahh ok that makes sense. Does any one know of any good tools for getting the calls? I know of Bis-SNP other than that I am unaware of any others.

Thanks
Leanne

[dpryan]

The only standalone application I've ever heard of is Bis-SNP. Since most of us who have written aligners include something with them (often making the calls as we go), there probably aren't a lot of options there.