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


I try to run qiime to join reads, with the script, with the next command: -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/", 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 • 387 views
ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 7 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.

ADD REPLYlink modified 7 months ago • written 7 months ago by RamRS20k

Sorry, I modified the question

ADD REPLYlink written 7 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 6 months ago by Marks40
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