I just installed the latest version of qiime: qiime2-2018.2 and when I run split_libraries_fastq.py I get the error:
Traceback (most recent call last): File "/Users/leahbriscoe/anaconda/bin/split_libraries_fastq.py", 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: split_libraries_fastq.py 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:
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?).