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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
