Question: Macs: Valueerror: Invalid Literal For Int() With Base 10: '1:N:0:'
0
gravatar for Nick
6.6 years ago by
Nick270
Spain
Nick270 wrote:

I got the above error when trying to run MACS 1.4.2 (I'm copying the parameter/output below). I ran previously the same sample/control with mfiold=32 but got no peaks. Than changed mfold to 10 and got this error. Does anyone know what is going on and what to do about it?

MACS input/output (error message is at the end):

========================================================

effective genome size = 1.00e+09

tag size = 40

band width = 300

model fold = 10

pvalue cutoff = 1.00e-05

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL181494.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL182298.1, plus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL180583.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL183373.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL192011.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL185054.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL178673.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL187281.1, plus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL181933.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL189987.1, plus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL185212.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL186088.1, plus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL184880.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL189261.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL190030.1, plus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL181273.1, plus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL191240.1, plus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL190257.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL176051.1, minus strand!

WARNING @ Sat, 13 Jul 2013 04:29:05: NO records for chromosome GL183262.1, minus strand!

....

and plenty of similar warnings about missing chromosomes

....

INFO @ Sat, 13 Jul 2013 04:29:31: #1.2 read input tags...

Traceback (most recent call last):

File "/home/g2main/linux3.2-x86_64/bin/macs", line 273, in <module>

main()

File "/home/g2main/linux3.2-x86_64/bin/macs", line 57, in main

(treat, control) = load_tag_files_options (options)

File "/home/g2main/linux3.2-x86_64/bin/macs", line 256, in load_tag_files_options

control = options.build(open2(options.cfile, gzip_flag=options.gzip_flag))

File "/home/g2main/linux3.2-x86_64/lib/python2.7/MACS/IO/__init__.py", line 1480, in build_fwtrack

(chromosome,fpos,strand) = self.__fw_parse_line(thisline)

File "/home/g2main/linux3.2-x86_64/lib/python2.7/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:'

chip-seq • 3.5k views
ADD COMMENTlink modified 3.5 years ago by paul.e.gradie100 • written 6.6 years ago by Nick270
0
gravatar for paul.e.gradie
3.5 years ago by
paul.e.gradie100
Australia/Melbourne/University of Melbourne
paul.e.gradie100 wrote:

For anyone who is finding this far down the road (this post is 3.1 years old by now)...

There is a decent chance that you may have the -f/--Format option set incorrectly.

Make sure this agrees with the file type you are loading in for analysis. -f BAM or -f BED, etc.

Cheers, Paul

ADD COMMENTlink written 3.5 years ago by paul.e.gradie100
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