multiple_join_paired_ends.py error in path

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Riley Hughes

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May 16, 2019, 10:29:30 AM5/16/19
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I am trying to run multiple_join_paired_ends.py but get the following error:
riley@kable-PowerEdge-T630:~$ multiple_join_paired_ends.py -i ~/Documents/Mock_Spike_In/cutadapt_trim -o ~/Documents/Mock_Spike_In/QIIME1/join_paired_ends --read1_indicator '_R1' --read2_indicator '_R2'
Traceback (most recent call last):
  File "/usr/local/bin/multiple_join_paired_ends.py", line 201, in <module>
    main()
  File "/usr/local/bin/multiple_join_paired_ends.py", line 198, in main
    close_logger_on_success=True)
  File "/usr/local/lib/python2.7/dist-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: join_paired_ends.py: /home/riley/Documents/Mock_Spike_In/cutadapt_trim/ZFeSFwM3_R1.fastq
Command run was:
 join_paired_ends.py  -f /home/riley/Documents/Mock_Spike_In/cutadapt_trim/ZFeSFwM3_R1.fastq -r /home/riley/Documents/Mock_Spike_In/cutadapt_trim/ZFeSFwM3_R2.fastq -o /home/riley/Documents/Mock_Spike_In/QIIME1/join_paired_ends/ZFeSFwM3_R1
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/usr/local/bin/join_paired_ends.py", line 178, in <module>
    main()
  File "/usr/local/bin/join_paired_ends.py", line 155, in main
    working_dir=output_dir)
  File "/usr/local/lib/python2.7/dist-packages/bfillings/fastq_join.py", line 207, in join_paired_end_reads_fastqjoin
    result = fastq_join_app(infile_paths)
  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 303, in __call__
    result_paths)
  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 325, in _handle_app_result_build_failure
    raise ApplicationError("Error constructing CommandLineAppResult.")
burrito.util.ApplicationError: Error constructing CommandLineAppResult.

The command halts after the first file. I have tried moving fastq_join.py to /usr/local/bin/, making it executable both there and in its original location, (in ./bfillings/), setting the working directory to /usr/local/bin/, adding ./bfillings to PATH but nothing is working. The only thing is when I set the working directory to /usr/local/bin/, I get a slightly different error:
Stderr
Traceback (most recent call last):
  File "/usr/local/bin/join_paired_ends.py", line 178, in <module>
    main()
  File "/usr/local/bin/join_paired_ends.py", line 155, in main
    working_dir=output_dir)
  File "/usr/local/lib/python2.7/dist-packages/bfillings/fastq_join.py", line 180, in join_paired_end_reads_fastqjoin
    HALT_EXEC=HALT_EXEC)
  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 201, in __init__
    self._error_on_missing_application(params)
  File "/usr/local/lib/python2.7/dist-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?

Any help would be appreciated!
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