I downloaded metaphlan2 using conda and I am attempting to use strainphlan to profile my samples at the strain level.
I have been following the instructions on this page:
I successfully completed the sample2markers.py step, however I cannot run step 3: Identify clades detected in the samples and build reference databases. The command i am using is:
strainphlan.py --ifn_samples p100_bowtie2_aligned.markers --output_dir markers/ --print_clades_only > clades.txt
Which results in the following error:
Traceback (most recent call last):
File “/mnt/nfs/home/30041036/.conda/envs/metaphlan2/bin/strainphlan.py”, line 1585, in
File “/mnt/nfs/home/30041036/.conda/envs/metaphlan2/bin/strainphlan.py”, line 1581, in strainphlan
File “/mnt/nfs/home/30041036/.conda/envs/metaphlan2/bin/strainphlan.py”, line 1365, in strainer
db = pickle.load(bz2.BZ2File(args[‘mpa_pkl’]))
File “/mnt/nfs/home/30041036/.conda/envs/metaphlan2/lib/python3.7/bz2.py”, line 92, in init
self._fp = _builtin_open(filename, mode)
IsADirectoryError: [Errno 21] Is a directory: ‘/mnt/nfs/home/30041036/.conda/envs/metaphlan2/bin/metaphlan_databases’
How can I fix this? I can’t see that anyone else has had similar issues. Also in step 4 --ifn_markers s__Eubacterium_siraeum.markers.fasta is used in the command, how do I generate this fasta file for the species I am interested in (e.g. staphylococcus aureus)?