Comments (7)
modules.amr.amr.amr('/datastore/2018-06-04-04-23-20-021208-ECI-2644_lcl.fasta') from amr
129911fc-0069-4375-82b5-05b977741dbc
Failed 6 minutes ago
Traceback (most recent call last):
File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job
rv = job.perform()
File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform
self._result = self.func(*self.args, **self.kwargs)
File "./modules/amr/amr.py", line 27, in amr
'-o', outputname])
File "/opt/conda/envs/backend/lib/python2.7/subprocess.py", line 168, in call
return Popen(*popenargs, **kwargs).wait()
File "/opt/conda/envs/backend/lib/python2.7/subprocess.py", line 390, in __init__
errread, errwrite)
File "/opt/conda/envs/backend/lib/python2.7/subprocess.py", line 1024, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
from spfy.
or maybe just a new interface
root@aa6de58fc93e:/app# rgi
usage: rgi <command> [<args>]
commands are:
main Runs rgi application
tab Creates a Tab-delimited from rgi results
parser Creates categorical .json files RGI wheel visualization. An input .json file containing the RGI results must be input.
load Loads CARD database json file
clean Removes BLAST databases and temporary files
galaxy Galaxy project wrapper
database Information on installed card database
rgi: error: too few arguments
root@aa6de58fc93e:/app# rgi main
usage: rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE
[-t {read,contig,protein,wgs}] [-a {DIAMOND,BLAST}]
[-n THREADS] [--include_loose] [--local] [--clean] [--debug]
[--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]
rgi main: error: argument -i/--input_sequence is required
from spfy.
removing overlapping rgi deps from the webserver env, since the conda update...
command will overwrite new versions with older ones.
kevin@kevin-ThinkPad-T510:~$ conda install -c bioconda rgi=4.0.3
Fetching package metadata .................
Solving package specifications: .
Package plan for installation in environment /home/kevin/miniconda2:
The following NEW packages will be INSTALLED:
biopython: 1.71-py27_0 conda-forge
diamond: 0.9.21-1 bioconda
filetype: 1.0.1-py_0 conda-forge
intel-openmp: 2018.0.3-0
libgfortran-ng: 7.2.0-hdf63c60_3
libopenblas: 0.2.20-h9ac9557_7
mkl: 2018.0.3-1
mkl_fft: 1.0.2-py27_0 conda-forge
mkl_random: 1.0.1-py27_0 conda-forge
numpy: 1.14.3-py27hcd700cb_2
numpy-base: 1.14.3-py27h0ea5e3f_1
prodigal: 2.6.3-0 bioconda
rgi: 4.0.3-py27_0 bioconda
The following packages will be UPDATED:
conda: 4.3.34-py27_0 conda-forge --> 4.5.4-py27_0 conda-forge
The following packages will be SUPERSEDED by a higher-priority channel:
conda-env: 2.6.0-h36134e3_1 --> 2.6.0-0 conda-forge
from spfy.
# Indices check.
df = pd.read_table(pickled_amr_tsv)
indices = df.index.values
> assert set(AMR_INDICES).issubset(set(indices))
E AssertionError: assert False
E + where False = <built-in method issubset of set object at 0x7fbceee796a8>(set([0, 1, 2, 3, 4, 5, ...]))
E + where <built-in method issubset of set object at 0x7fbceee796a8> = set(['Best_Hit_ARO', 'CUT_OFF', 'ORF_ID', 'ORIENTATION', 'START', 'STOP']).issubset
E + where set(['Best_Hit_ARO', 'CUT_OFF', 'ORF_ID', 'ORIENTATION', 'START', 'STOP']) = set(['ORF_ID', 'START', 'STOP', 'ORIENTATION', 'CUT_OFF', 'Best_Hit_ARO'])
E + and set([0, 1, 2, 3, 4, 5, ...]) = set(array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,\n ...50,\n 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]))
from spfy.
Looks like RGI now identifies fewer targets:
E AssertionError: assert 1878 == 2007
E + where 1878 = length('/home/travis/build/superphy/spfy/app/tests/ecoli/GCA_001894495.1_ASM189449v1_genomic.fna_rgi.ttl')
E + and 2007 = length('tests/refs/GCA_001894495.1_ASM189449v1_genomic.fna_rgi.ttl')
from spfy.
Update looks good as of 1a86201 . Updating tests and pinning env versions now...
from spfy.
done in #305
from spfy.
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from spfy.