Question: qiime error join read
0
gravatar for genomebiomex
16 months ago by
genomebiomex0 wrote:

Hello

I try to run qiime to join reads, with the script join_paired_ends.py, with the next command:

join_paired_ends.py -f SM000720-1_S1_L001_R1_001.fastq -r SM000720-1_S1_L001_R2_001.fastq -o join_joined_SM00720 -j 30 -p 10
------------------------------------------------------------------------

but the program has an error


##error ##

/miniconda3/envs/qiime1/lib/python2.7/site-packages/burrito-0.9.1-py2.7.egg/burrito/util.py", line 468, in _error_on_missing_application
burrito.util.ApplicationNotFoundError: Cannot find fastq-join. Is it installed? Is it in your path?

The program is in path currently, what happened?

qiime • 698 views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 16 months ago by genomebiomex0

Why is this a tutorial post? It is a question. Also, please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink modified 16 months ago • written 16 months ago by RamRS25k

Sorry, I modified the question

ADD REPLYlink written 16 months ago by genomebiomex0

When you say program, you are referring to fastq-join? Make sure it was installed with miniconda. I'm not really sure how conda would handle different python versions and a program installed outside of conda. It should play nice but who knows. Also if you can provide the output of echo $PATH that would be great.

ADD REPLYlink written 15 months ago by Amar620
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