Question: MACS error while analyzing ChIP-seq peakes
0
gravatar for dorota.komar
14 months ago by
dorota.komar10
Spain
dorota.komar10 wrote:

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!

macs chip-seq • 394 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by dorota.komar10

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 callpeak instead.

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.

ADD REPLYlink written 14 months ago by Devon Ryan1.9k
0
gravatar for dorota.komar
14 months ago by
dorota.komar10
Spain
dorota.komar10 wrote:

Thank you a lot! I will try with MACS2 callpeak :)

ADD COMMENTlink written 14 months ago by dorota.komar10

I second that you should be using the newer version of this tool suite.

That said, this error is usually due to spaces in the input SAM dataset's sequence names (unmapped reads will retain spaces). Compress the inputs with SAM-to-BAM to avoid this issue whether using MACS or MACS2. Alternatively, you could filter out the unmapped reads.

Hope that helps! Jen, Galaxy team

ADD REPLYlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 133 users visited in the last hour