No module named qiime.util

I just installed the latest version of qiime: qiime2-2018.2 and when I run I get the error:

Traceback (most recent call last): File "/Users/leahbriscoe/anaconda/bin/", line 19, in <module> from qiime.util import parse_command_line_parameters, make_option, gzip_open ImportError: No module named qiime.util

after running the command: FASTQ_files/SRR5908980.fastq --barcode_type 'not-barcoded'

I’m wondering if it’s because I did a pip install (which used the old qiime) right before this one. I deleted all the qiime files I thought were relevant but I think there might still be issues.


QIIME2 represents a very different way of approaching analyses and interacting with data. The QIIME1 model of calling a script with a bunch of arguments is gone - hence why you are receiving an error, you are calling a QIIME1 script but QIIME1 no longer exists. IMHO the new model is much easier once you get past the initial changes. I would strongly recommend taking a look a the QIIME2 tutorial to get a sense of what the new commands look like but as an examples: FASTQ_files/SRR5908980.fastq --barcode_type 'not-barcoded'

Would look like the following in QIIME2

first you would load your files into a .qza file:

qiime tools import \
  --type EMPSingleEndSequences \
  --input-path FASTQ_files\
  --output-path emp-single-end-sequences.qza

Then demultiplex

qiime demux emp-single \
  --i-seqs emp-single-end-sequences.qza \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-column BarcodeSequence \
  --o-per-sample-sequences demux.qza

This is taken from the tutorial so you will need to adapt the commands to exactly what you need, but I just wanted to provide an example of the usage.

You can find the tutorial here


Thanks for clarifying that! Since I have already joined reads that are also already demultiplexed, I’m trying QIIME 1 now.

Assuming you are still seeing that error, I think something may have gone wrong in your conda environment.

QIIME 2 is installed into it’s own environment, so it shouldn’t be impacting your QIIME 1 scripts at all, however you do have QIIME 1 installed in the “root” environment, which can be tricky to get right.

I would recommend uninstalling conda and starting over with the QIIME 1 (and 2) installation, making sure each is in it’s own conda environment so that they can’t interact with other programs (which is maybe what’s happening?).

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