We get the following error when trying to run MACS in our local installation of 
Galaxy:

INFO  @ Mon, 30 Apr 2012 09:02:14:
# ARGUMENTS LIST:
# name = MACS_in_Galaxy
# ChIP-seq file = /proj/galaxy/000/dataset_552.dat
# control file = None
# effective genome size = 2.70e+09
# tag size = 36
# band width = 300
# model fold = 32
# pvalue cutoff = 1.00e-05
# Ranges for calculating regional lambda are : 1000,5000,10000
INFO  @ Mon, 30 Apr 2012 09:02:14: #1 read tag files...
INFO  @ Mon, 30 Apr 2012 09:02:14: #1 read treatment tags...
Traceback (most recent call last):
  File "/nas02/apps/python-2.6.5/bin/macs", line 238, in <module>
    main()
  File "/nas02/apps/python-2.6.5/bin/macs", line 53, in main
    (treat, control) = _load_tag_files_options (options)
  File "/nas02/apps/python-2.6.5/bin/macs", line 211, in _load_tag_files_options
    treat = load_tag_file(options.tfile,options.format)
  File "/nas02/apps/python-2.6.5/bin/macs", line 231, in load_tag_file
    raise Exception("Format \"%s\" cannot be recognized!" % (format))
Exception: Format "SAM" cannot be recognized!

Does anyone know what causes this? We are using MACS-1.3.2.

Mike Waldron

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