Error in join_paired_ends.py

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Kiran

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Jan 4, 2018, 1:09:32 AM1/4/18
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Hi all,

While using ubuntu 17.04  join_paired_ends.py was working fine,but after installing ubuntu 17.10 it is not working.??

Error:

Traceback (most recent call last):
  File "/home/saikiran/anaconda2/bin/join_paired_ends.py", line 178, in <module>
    main()
  File "/home/saikiran/anaconda2/bin/join_paired_ends.py", line 155, in main
    working_dir=output_dir)
  File "/home/saikiran/anaconda2/lib/python2.7/site-packages/bfillings/fastq_join.py", line 180, in join_paired_end_reads_fastqjoin
    HALT_EXEC=HALT_EXEC)
  File "/home/saikiran/anaconda2/lib/python2.7/site-packages/burrito/util.py", line 201, in __init__
    self._error_on_missing_application(params)
  File "/home/saikiran/anaconda2/lib/python2.7/site-packages/burrito/util.py", line 468, in _error_on_missing_application
    "Is it in your path?" % command)
burrito.util.ApplicationNotFoundError: Cannot find fastq-join. Is it installed? Is it in your path?


I have tried
sudo apt install ea-utils
then

The following packages have unmet dependencies:
 ea-utils : Depends: r-cran-getopt but it is not going to be installed
            Depends: r-cran-hmisc but it is not going to be installed
            Depends: r-cran-formula but it is not going to be installed
            Depends: r-cran-ggplot2 but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

Pls help


Colin Brislawn

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Jan 5, 2018, 9:39:29 PM1/5/18
to Qiime 1 Forum
Hello Kiran,

After installing a new version of Ubuntu Linux, you should probably install Qiime again using anaconda.

Or, have you considered installing Qiime 2? This new version of qiime is being actively developed and improved, and now is a great time to upgrade.

Colin

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