Question: (Closed) I have some problems to deal with macs.
gravatar for jsleecsbl
2.3 years ago by
jsleecsbl0 wrote:


I recently followed the protocol of m6A sequencing which is published in 2013 (Dominissini, Dan, et al. "Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing." Nature protocols 8.1 (2013): 176-189.). And I got two problems. Those troubles are found in running macs. At first, according to above reference paper, they used "--to-small" parameter. However, in my case, my computer said there isn't such option called "--to-small". Next, if I typed like this "macs14 -t IP.sam -c Input.sam --name=m6A --format="SAM" --gsize=282000000 --tsize=36 --nomodel --shiftsize=50 -w -S 2 > macs.out &", then there are some errors found like as follows.


# name = m6A

# format = SAM

# ChIP-seq file = IP.sam

# control file = Input.sam

# effective genome size = 2.82e+08

# band width = 300

# model fold = 10,30

# pvalue cutoff = 1.00e-05

# Large dataset will be scaled towards smaller dataset.

# Range for calculating regional lambda is: 1000 bps and 10000 bps

INFO @ Wed, 17 Aug 2016 10:26:59: #1 read tag files...

INFO @ Wed, 17 Aug 2016 10:26:59: #1 read treatment tags...

Traceback (most recent call last):

File "/usr/local/bin/macs14", line 366, in <module> main()

File "/usr/local/bin/macs14", line 60, in main (treat, control) = load_tag_files_options (options)

File "/usr/local/bin/macs14", line 335, in load_tag_files_options ttsize = tp.tsize()

File "/usr/local/lib/python2.7/dist-packages/MACS14/IO/", line 647, in tsize (chromosome,fpos,strand) = self.__fw_parse_line(thisline)

File "/usr/local/lib/python2.7/dist-packages/MACS14/IO/", line 684, in __fw_parse_line bwflag = int(thisfields[1])

ValueError: invalid literal for int() with base 10: '-'

This is my first time to use macs, so if anyone helps me, I'll very appreciate it.

Thank you

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by jsleecsbl0


I suggest you to post your problem on more than here since it's not a galaxy problem. You will find more help by asking directly the developers.

ADD REPLYlink written 2.3 years ago by Rob50

Thank you, I'll do like you said.

ADD REPLYlink written 2.3 years ago by jsleecsbl0

Hello jsleecsbl!

We believe that this post does not fit the main topic of this site.

Not Galaxy related.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 2.3 years ago by James Taylor470
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