ModuleNotFoundError: No module named 'readfq' arises during the execution of kmergenie

Question

[yuanym]

$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.

Answer 1

[Kevin Blighe]

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