ModuleNotFoundError: No module named 'readfq' arises during the execution of kmergenie
$cat kmer_list_files
D31-10A_1.qc.fq.gz
D31-10A_2.qc.fq.gz
$ kmergenie kmer_list_files --diploid
/home/cdbi1/miniconda3/envs/gensize/bin/kmergenie:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
running histogram estimation
list of reads:
D31-10A_1.qc.fq.gz
D31-10A_2.qc.fq.gz
Traceback (most recent call last):
File "/home/cdbi1/miniconda3/envs/gensize/bin/kmergenie", line 303, in <module>
best_k = execute_once(arguments_passed_list, first_pass=first_pass)
File "/home/cdbi1/miniconda3/envs/gensize/bin/kmergenie", line 279, in execute_once
ntcard_wrapper(k_interval)
File "/home/cdbi1/miniconda3/envs/gensize/bin/kmergenie", line 221, in ntcard_wrapper
max_read_length = get_read_length(read_file_list)
File "/home/cdbi1/miniconda3/envs/gensize/bin/kmergenie", line 147, in get_read_length
from readfq import readfq
ModuleNotFoundError: No module named 'readfq'
Has anyone encountered this kind of issue? How can it be resolved? Thank you.
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1 answer
Have you tried to install readfq? - conda install -c bioconda readfq
Failing that, I would re-install kmergenie, but via conda:
conda install -c bioconda kmergenie
Kevin
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