Question: Help! Galaxy MACS Peak Calling-
gravatar for supark2013
2.6 years ago by
United States
supark20130 wrote:
Hi I have aligned my ChIP-Seq and Input to genome and created SAM files. I tried to do peak calling with MACS but I am keep getting bellow error message. I am new to the system and don't know what's the problem. Could anyone please help me understand what's the problem here/solution to it? Thank you,

For settings, I did
  1. “yes” to Parse xls files into into distinct interval files
  2. “Save” for Save shifted raw tag count at every bp into a wiggle file
  3. Build model: choose “do not build the shifting model
INFO  @ Wed, 19 Aug 2015 20:53:28: 
# name = MACS_in_Galaxy
# format = SAM
# ChIP-seq file = /galaxy-repl/main/files/012/212/dataset_12212213.dat
# control file = /galaxy-repl/main/files/012/212/dataset_12212223.dat
# effective genome size = 2.70e+09
# tag size = 49
# band width = 300
# model fold = 32
# pvalue cutoff = 1.00e-05
# Ranges for calculating regional lambda are : peak_region,1000,5000,10000 
INFO  @ Wed, 19 Aug 2015 20:53:28: #1 read tag files... 
INFO  @ Wed, 19 Aug 2015 20:53:28: #1 read treatment tags... 
Traceback (most recent call last):
  File "/galaxy/main/deps/macs/", line 273, in <module>
  File "/galaxy/main/deps/macs/", line 57, in main
    (treat, control) = load_tag_files_options (options)
  File "/galaxy/main/deps/macs/", line 252, in load_tag_files_options
    treat =, gzip_flag=options.gzip_flag))
  File "/galaxy/main/deps/macs/", line 1480, in build_fwtrack
    (chromosome,fpos,strand) = self.__fw_parse_line(thisline)
  File "/galaxy/main/deps/macs/", line 1500, in __fw_parse_line
    bwflag = int(thisfields[1])
ValueError: invalid literal for int() with base 10: '1:N:0'
peak calling galaxy macs • 813 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson24k • written 2.6 years ago by supark20130
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson24k wrote:


Convert the SAM datasets to BAM format, then re-run MACS. The problem is almost certain with spaces in the original FASTQ input datasets "sequence" identifiers. (MACS does not process these well in SAM format, but just fine in binary BAM format).

Please let us know if this does not work out, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson24k
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