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  • MACS: ValueError: invalid literal for int() with base 10: '1:N:0:'

    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

    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:'

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