Hi, I am analyzing my ChIP-seq data. I am pretty sure I am following the workflow correctly, because I obtained nice results for one tissue type. In the second tissue type I, however, got an error while trying to use MACS tool. It is kind of surprising, because I can analyze the data fine while using MACS analysis in SeqMonk, but while standard galaxy workflow and standard SeqMonk give different results I would like to have galaxy analysis to compare the peaks.
The error says: INFO @ Wed, 26 Apr 2017 05:32:23:
ARGUMENTS LIST:
name = MACS_in_Galaxy
format = SAM
ChIP-seq file = /galaxy-repl/main/files/019/699/dataset_19699447.dat
control file = /galaxy-repl/main/files/019/699/dataset_19699446.dat
effective genome size = 2.70e+09
tag size = 45
band width = 350
model fold = 32
pvalue cutoff = 1.00e-05
Ranges for calculating regional lambda are : peak_region,1000,5000,10000
INFO @ Wed, 26 Apr 2017 05:32:23: #1 read tag files... INFO @ Wed, 26 Apr 2017 05:32:23: #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:CTTGTA'
Can someone explain to me what does it mean?
Thank you very much in advance!
There's no reason to use such an old version of MACS (I don't know why this is even still available on the main Galaxy instance). Please use
MACS2 callpeakinstead.For what it's worth, the error is due to some sort of incorrectly formatted input, but since this version is more than 6 years old there's no reason to bother trying to debug it.