geronimp / graftm-docker Goto Github PK

First time using GraftM and I tried to use the docer but I run this and get an error:

docker pull wwood/graftm:v0.11.1
v0.11.1: Pulling from wwood/graftm
ec41389a8271: Pull complete
Digest: sha256:dc81a3f9cab8d3015a9c2dcaa7a627471b9dfbe4df2de6b3b03f88b15d3e1d72
Status: Downloaded newer image for wwood/graftm:v0.11.1

docker run -u $(id -u):$(id -g) -v pwd:/data wwood/graftm:v0.11.1 graft
Traceback (most recent call last):
File "/gnu/store/76g5nc8c0qly1i4za6idafyynj3lvail-graftm-0.11.1/bin/..graftM-real-real", line 39, in
from graftm.run import Run
File "/gnu/store/76g5nc8c0qly1i4za6idafyynj3lvail-graftm-0.11.1/lib/python2.7/site-packages/graftm/run.py", line 14, in
from graftm.summarise import Stats_And_Summary
File "/gnu/store/76g5nc8c0qly1i4za6idafyynj3lvail-graftm-0.11.1/lib/python2.7/site-packages/graftm/summarise.py", line 2, in
from biom.table import Table
File "/gnu/store/2jwm8awn421ag1hh7gvjwbyh5x881aq4-python2-biom-format-2.1.6/lib/python2.7/site-packages/biom/init.py", line 51, in
from .table import Table
File "/gnu/store/2jwm8awn421ag1hh7gvjwbyh5x881aq4-python2-biom-format-2.1.6/lib/python2.7/site-packages/biom/table.py", line 189, in
import pandas as pd
File "/gnu/store/sj17h05k5jkzvnp4s8fvlba0mdxpylmd-python2-pandas-0.19.2/lib/python2.7/site-packages/pandas/init.py", line 39, in
from pandas.core.api import *
File "/gnu/store/sj17h05k5jkzvnp4s8fvlba0mdxpylmd-python2-pandas-0.19.2/lib/python2.7/site-packages/pandas/core/api.py", line 10, in
from pandas.core.groupby import Grouper
File "/gnu/store/sj17h05k5jkzvnp4s8fvlba0mdxpylmd-python2-pandas-0.19.2/lib/python2.7/site-packages/pandas/core/groupby.py", line 40, in
from pandas.core.frame import DataFrame
File "/gnu/store/sj17h05k5jkzvnp4s8fvlba0mdxpylmd-python2-pandas-0.19.2/lib/python2.7/site-packages/pandas/core/frame.py", line 72, in
from pandas.core.series import Series
File "/gnu/store/sj17h05k5jkzvnp4s8fvlba0mdxpylmd-python2-pandas-0.19.2/lib/python2.7/site-packages/pandas/core/series.py", line 2974, in
import pandas.tools.plotting as _gfx # noqa
File "/gnu/store/sj17h05k5jkzvnp4s8fvlba0mdxpylmd-python2-pandas-0.19.2/lib/python2.7/site-packages/pandas/tools/plotting.py", line 34, in
import pandas.tseries.converter as conv
File "/gnu/store/sj17h05k5jkzvnp4s8fvlba0mdxpylmd-python2-pandas-0.19.2/lib/python2.7/site-packages/pandas/tseries/converter.py", line 7, in
import matplotlib.units as units
File "/gnu/store/sff2s1n5pzv1fyabfv3l37q4i07lr3yw-python2-matplotlib-2.0.2/lib/python2.7/site-packages/matplotlib/init.py", line 1182, in
rcParams = rc_params()
File "/gnu/store/sff2s1n5pzv1fyabfv3l37q4i07lr3yw-python2-matplotlib-2.0.2/lib/python2.7/site-packages/matplotlib/init.py", line 1015, in rc_params
fname = matplotlib_fname()
File "/gnu/store/sff2s1n5pzv1fyabfv3l37q4i07lr3yw-python2-matplotlib-2.0.2/lib/python2.7/site-packages/matplotlib/init.py", line 825, in matplotlib_fname
configdir = _get_configdir()
File "/gnu/store/sff2s1n5pzv1fyabfv3l37q4i07lr3yw-python2-matplotlib-2.0.2/lib/python2.7/site-packages/matplotlib/init.py", line 680, in _get_configdir
return _get_config_or_cache_dir(_get_xdg_config_dir())
File "/gnu/store/sff2s1n5pzv1fyabfv3l37q4i07lr3yw-python2-matplotlib-2.0.2/lib/python2.7/site-packages/matplotlib/init.py", line 657, in _get_config_or_cache_dir
return _create_tmp_config_dir()
File "/gnu/store/sff2s1n5pzv1fyabfv3l37q4i07lr3yw-python2-matplotlib-2.0.2/lib/python2.7/site-packages/matplotlib/init.py", line 577, in _create_tmp_config_dir
tempdir = tempfile.gettempdir()
File "/gnu/store/0n8ni2ldvyz5yd488cidzi3via7jk7pw-python-2.7.13/lib/python2.7/tempfile.py", line 275, in gettempdir
tempdir = _get_default_tempdir()
File "/gnu/store/0n8ni2ldvyz5yd488cidzi3via7jk7pw-python-2.7.13/lib/python2.7/tempfile.py", line 217, in _get_default_tempdir
("No usable temporary directory found in %s" % dirlist))
IOError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/']

Hi,

I am a new user of graftM. Running using docker.
When I try to run graftM create to build a package I receive the following errors.

> docker run -v pwd:/data wwood/graftm:v0.13.1 create --sequences /Users/e/Documents/graftm_test/bsh_sequences.fasta --taxonomy /Users/e/Documents/graftm_test/bsh_taxonomy_file2.txt --output bsh_graftm_package.gpkg --log bsh_log.txt
Traceback (most recent call last):
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/bin/.graftM-real", line 415, in
Run(args).main()
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/lib/python3.7/site-packages/graftm/run.py", line 681, in main
threads = self.args.threads
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/lib/python3.7/site-packages/graftm/create.py", line 593, in main
taxonomy_definition = GreenGenesTaxonomy.read_file(taxonomy).taxonomy
File "/gnu/store/jcxdrw6c6z7n9q9wwqjyirk0lxgm715x-graftm-0.13.1/lib/python3.7/site-packages/graftm/greengenes_taxonomy.py", line 51, in read_file
with open(input_filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/e/Documents/graftm_test/bsh_taxonomy_file2.txt'

Even though the file clearly is in my current working directory:
Directory: C:\Users\e\Documents\graftm_test> ls
Mode LastWriteTime Length Name

-a---- 28/10/2020 10:48 AM 214479 bsh_sequences.fasta
-a---- 28/10/2020 12:05 PM 27362 bsh_taxonomy_file1.txt
-a---- 28/10/2020 1:55 PM 27362 bsh_taxonomy_file2.txt

Happens whether I run this on PC or MAC.

Including --user $(id -u):$(id -g) doesn't change anything other than generating the additional error "The term 'id' is not recognized as the name of a cmdlet, function, script file, or operable program."

Thanks for any help in understanding how to overcome this error.
Erin

Hello,

I am trying to run GraftM containers with Singularity. I have successfully pulled an image with:

singularity pull docker://wwood/graftm

but execution fails. I have tried:

$ singularity exec graftm_latest.sif ls
WARNING: passwd file doesn't exist in container, not updating
WARNING: group file doesn't exist in container, not updating
FATAL:   exec /.singularity.d/actions/exec failed: no such file or directory

and

singularity inspect graftm_latest.sif 
FATAL:   exit status 255

Thanks for your help!

Domenico

Greetings,

The URL for HMMER needs to be updated in the Dockerfile -- http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz

Cheers,