qiime
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biocore
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
A user was trying to start a QIIME Visualization app session on BaseSpace, but was unable to start analysis. The specific error is: "This is not a valid spreadsheet keey,...
Seeing many of these coming from `core_diversity_analysis.py`: ``` bash can't invoke "event" command: application has been destroyed while executing "event generate $w " (procedure "ttk::ThemeChanged" line 6) invoked from within...
We downloaded clustered rDNA files from MG-RAST and we would like to annotate samples but the first step "split_libraries.py" is asking for mapping file for barcodes to demultiplex sequences. Since...
I did the taxonomy assignment using local RDP database,but encountered the following error. The sad thing is I am not familiar with python script. Can Someone help me! Traceback (most...
hi, I m using QIIME for OTU identification. I have raw paired fastq files. i do not have any information of barcode and linker primer .So i decided to create...
There is a significant number of links in the documentation that are broken. I point out some examples only: https://github.com/biocore/qiime/blob/master/doc/documentation/script_index.rst it says "This page has moved HERE" and here is...
I know QIIME1 support ends soon, but I wanted to record this information somewhere in case people still using it run in to this problem. This also seems like a...
When `pick_otus.py` calls `uclust` it uses /tmp/ vs. using the temp_dir in the qiime configuration, an example: `uclust --input /tmp/UclustExactMatchFilterlS4C2v.fasta --id 0.97 --tmpdir /tmp --rev --w 12 --stepwords 20 --usersort...
...I think... I'm no Python God, but as I understand the code it is using mkstemp which itself makes the temporary file in /tmp unles TMPDIR, TEMP or TMP environment...
Specifically, the slicing approach of these lines: https://github.com/biocore/qiime/blob/master/qiime/extract_barcodes.py#L412 https://github.com/biocore/qiime/blob/master/qiime/extract_barcodes.py#L414 creates a problem with the length of the barcode is zero, should be adjusted to use the len(sequence)-length of barcode to...
