After loading up MetaPhlAn2 (8991e05c44e4) from toolshed and attaching db_v20, I tried running a few fasta files on it, including the tool's test-data/input_sequences.fasta file, but after about a minute of churning I keep getting this error:
Fatal error: Exit code 1 () … Traceback (most recent call last): File "/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_ metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 1172, in <module> tree = TaxTree( mpa_pkl, ignore_markers ) File "/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_ metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 857, in __init__ clades_txt = ((l.strip().split("|"),n) for l,n in mpa_pkl['taxonomy'].items()) AttributeError: 'list' object has no attribute 'items'
I believe the database is connected properly, but would the tool run for a while even if it wasn't? It seems like the mpa_pkl file data is loaded via the --mpa_pkl attribute as in tool command line:
which bowtie2 || exit 200) && metaphlan2.py /galaxy_data/production1/files/013/dataset_13546.dat -o /galaxy_data/production1/files/013/dataset_13547.dat --input_type fasta --bowtie2_exe `which bowtie2` --bowtie2db /usr/local/packages/metaphlan2/db_v20/mpa_v20_m200 --mpa_pkl /usr/local/packages/metaphlan2/db_v20/mpa_v20_m200".pkl" --no_map -t rel_ab --tax_lev a --min_cu_len 2000 --min_alignment_len 0 --stat_q 0.1 -s /galaxy_data/production1/files/013/dataset_13548.dat
Tool's xml file does a touch of funny business with the mpa_v20_m200".pkl" file name parameter, but I guess that works if no one else has a problem with it.
Thx for any info,
Damion