Question: Help! Galaxy MACS Peak Calling-
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supark2013 • 0 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
- “yes” to Parse xls files into into distinct interval files
- “Save” for Save shifted raw tag count at every bp into a wiggle file
- Build model: choose “do not build the shifting model
INFO @ Wed, 19 Aug 2015 20:53:28:
# ARGUMENTS LIST:
# 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/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/bin/macs", line 273, in <module>
main()
File "/galaxy/main/deps/macs/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/bin/macs", line 57, in main
(treat, control) = load_tag_files_options (options)
File "/galaxy/main/deps/macs/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/bin/macs", line 252, in load_tag_files_options
treat = options.build(open2(options.tfile, gzip_flag=options.gzip_flag))
File "/galaxy/main/deps/macs/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/lib/python/MACS/IO/__init__.py", line 1480, in build_fwtrack
(chromosome,fpos,strand) = self.__fw_parse_line(thisline)
File "/galaxy/main/deps/macs/1.3.7.1/devteam/package_macs_1_3_7_1/a7ea583a35d2/lib/python/MACS/IO/__init__.py", line 1500, in __fw_parse_line
bwflag = int(thisfields[1])
ValueError: invalid literal for int() with base 10: '1:N:0'
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modified 3.3 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
3.3 years ago by
supark2013 • 0
