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' -- Chris Scharer, PhD Post-doctoral Fellow Laboratory of Dr. Jeremy Boss Dept of Immunology and Microbiology Emory University Atlanta GA 30322 Ph: 404-727-5959
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
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
Hi Chris, It appears that MACS does not properly handle whitespace characters in sequence identifiers. We'll look into a more streamlined way to handle this issue, but in the mean time, the easiest way to fix this issue is to use the FASTQ manipulation tool before mapping your data, similar to this screenshot (the 'From' box contains a space): You may also want to double-check the source encoding of these uploaded reads; I suspect that the quality scores have already been converted to the Sanger format before you uploaded them to Galaxy. Please let us know if we can be of further assistance. Thanks for using Galaxy, Dan On Dec 7, 2010, at 9:06 AM, Jennifer Jackson wrote:
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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
participants (3)
-
Christopher Scharer -
Daniel Blankenberg -
Jennifer Jackson