Problems using count_seqs.py with joined reads

[andso17]

I am pretty new to using these tools, so I hope I am not an inconvenience.

I am having problems with processing of an outputfile of joined reads, processed with the fastq-join from ea-utils. When running the following command I get an error, that seems to originate from failed import of files:

count_seqs.py -i join

(here 'join' is the name of the file of the joined, paired reads generated via ea-utils)

The error message looks like this:

Traceback (most recent call last):
File "/data/miniconda3/envs/qiime/bin/count_seqs.py", line 13, in
from qiime.util import (parse_command_line_parameters,
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime/util.py", line 49, in
from skbio.util import remove_files, create_dir
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/init.py", line 15, in
import skbio.io
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/io/init.py", line 309, in
import_module('skbio.io.clustal')
File "/data/miniconda3/envs/qiime/lib/python2.7/importlib/init.py", line 37, in import_module
import(name)
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/io/clustal.py", line 123, in
from skbio.alignment import Alignment
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/alignment/init.py", line 230, in
from ._alignment import Alignment, SequenceCollection, StockholmAlignment
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 21, in
from skbio.stats.distance import DistanceMatrix
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/stats/distance/init.py", line 193, in
from ._base import (DissimilarityMatrixError, DistanceMatrixError,
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/stats/distance/_base.py", line 17, in
from IPython.core.pylabtools import print_figure
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/IPython/init.py", line 48, in
from .core.application import Application
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/IPython/core/application.py", line 23, in
from traitlets.config.application import Application, catch_config_error
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/traitlets/config/init.py", line 6, in
from .application import *
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/traitlets/config/application.py", line 17, in
from decorator import decorator
File "/data/miniconda3/envs/qiime/lib/python2.7/site-packages/decorator.py", line 162
print('Error in generated code:', file=sys.stderr)
^

I would be very grateful for any help on the matter

[andso17]

Sorry, the arrow (last line) is supposed to point at '='. Below the arrow, this error-message is printed: "SyntaxError: invalid syntax"