Hi Chris,
This is the second report of a recent problem with MACS. If you have
time, please send us a history with the problem in it. Use: Options ->
Share or Publish -> Make History Accessible via Link and email the link
back to me. Also please send along any special settings made when using
the tool.
Thanks for reporting the issue and we look forward to your reply.
Hopefully we will be able to quickly determine & correct any issues,
Best!
Jen
Galaxy team
On 11/11/10 7:23 AM, Christopher Scharer wrote:
Hi,
I recently mapped some ChIP-seq data to the mm8 version of the mouse
genome with Bowtie to create a SAM file. However, I can not run MACS on
the mapped data because I keep getting the error below. Any suggestions??
Thanks,
Chris
Messages from MACS:
INFO @ Thu, 11 Nov 2010 10:07:30:
# ARGUMENTS LIST:
# name = MACS_in_Galaxy
# format = SAM
# ChIP-seq file =
/galaxy/home/g2main/galaxy_main/database/files/001/727/dataset_1727796.dat
# control file = None
# effective genome size = 2.70e+09
# tag size = 25
# band width = 300
# model fold = 32
# pvalue cutoff = 1.00e-05
# Ranges for calculating regional lambda are : peak_region,1000,5000,10000
INFO @ Thu, 11 Nov 2010 10:07:30: #1 read tag files...
INFO @ Thu, 11 Nov 2010 10:07:30: #1 read treatment tags...
INFO @ Thu, 11 Nov 2010 10:07:43: 1000000
INFO @ Thu, 11 Nov 2010 10:07:57: 2000000
INFO @ Thu, 11 Nov 2010 10:08:08: 3000000
INFO @ Thu, 11 Nov 2010 10:08:21: 4000000
INFO @ Thu, 11 Nov 2010 10:08:33: 5000000
Traceback (most recent call last):
File "/home/g2main/linux2.6-x86_64/bin/macs", line 273, in
main()
File "/home/g2main/linux2.6-x86_64/bin/macs", line 57, in main
(treat, control) = load_tag_files_options (options)
File "/home/g2main/linux2.6-x86_64/bin/macs", line 252, in
load_tag_files_options
treat = options.build(open2(options.tfile, gzip_flag=options.gzip_flag))
File "/home/g2main/linux2.6-x86_64/lib/python2.6/MACS/IO/__init__.py",
line 1480, in build_fwtrack
(chromosome,fpos,strand) = self.__fw_parse_line(thisline)
File "/home/g2main/linux2.6-x86_64/lib/python2.6/MACS/IO/__init__.py",
line 1500, in __fw_parse_line
bwflag = int(thisfields[1])
ValueError: invalid literal for int() with base 10: 'CTCF:7:185:443:687'
--
Jennifer Jackson
http://usegalaxy.org