Sofia P
Hi,
I am trying to run compare_categories.py on my data but am getting this error. Can someone please suggest how to fix this? Thanks!
MacQIIME user:biom $ compare_categories.py --method adonis -i unweighted_unifrac_dm.txt -m dietary_mapping_file.txt -c FiberCategory,FruitCategory,Wholegrain,Vegetables -o adonis_out -n 999
Traceback (most recent call last):
File "/macqiime/anaconda/bin/compare_categories.py", line 189, in <module>
main()
File "/macqiime/anaconda/bin/compare_categories.py", line 185, in main
categories, opts.num_permutations, out_dir)
File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/compare_categories.py", line 146, in compare_categories
rex(command_args, '%s.r' % method)
File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/util.py", line 1968, in __call__
(exit_status, command, stdout, stderr))
burrito.util.ApplicationError: Unacceptable application exit status: 1
command: cd "/Volumes/LaCie/biom/"; R --slave --args --source_dir /macqiime/anaconda/lib/python2.7/site-packages/qiime/support_files/R -d unweighted_unifrac_dm.txt -m dietary_mapping_file.txt -c FiberCategory -o adonis_out -n 999 < /macqiime/anaconda/lib/python2.7/site-packages/qiime/support_files/R/adonis.r
stdout:
stderr:
Warning message:
package ‘optparse’ was built under R version 3.1.3
Warning messages:
1: package ‘vegan’ was built under R version 3.1.3
2: package ‘permute’ was built under R version 3.1.3
3: package ‘lattice’ was built under R version 3.1.3
Error in objects[[i]][, IDs] : subscript out of bounds
Calls: remove.nonoverlapping.samples
Execution halted
