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'

Hello Chris, Are you still having problems? Would you have time send a link to your history? Use Options -> Share or Publish -> click to share the link and email back (to me) and we will provide feedback. Thanks! 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 _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user