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On the WildIris cluster we have downloaded the data resources from here: https://docs.qiime2.org/2022.8/data-resources/# and https://docs.qiime2.org/2023.2/tutorials/feature-classifier/
When you load the qiime2/<version> module, it sets a QIIME_DATA_RESOURCES environment variable, that can be used to view/access the data resources.
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| title | Example use of QIIME_DATA_RESOURCES environment variable: |
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[salexan5@wilog01 ~]$ module load qiime2/2023.5
[salexan5@wilog01 ~]$ echo $QIIME_DATA_RESOURCES
/apps/u/opt/qiime2/data
[salexan5@wilog01 ~]$ ls $QIIME_DATA_RESOURCES
gg_12_1085_otus.tar.gz fasta gg_13_8_otus.tar.gz silva-138gg-13-8-99-nb-weighted-classifier.qza
gg_13_5_otus.tar.gz silva-138-99-515-806-nb-classifier.qza
85_otus.qza gg_13_8_otus_4feb2011.tar.tgzgz silva-138-99-seqsnb-515-806classifier.qza
gg-13-8-99-515-806-nb-classifier.qza85_otu_taxonomy.txt sepp-refs-gg-13-8.qza silva-138-99-seqs.qza
gg-13-8-99-515-806-nb-weighted-classifier.qza sepp-refs-silva-128.qza gg_otus_4feb2011.tgz silva-138-99-taxnb-515weighted-806classifier.qza
gg-13-8-99-nb-classifier.qza silva-138-99-515-806-nb-classifier.qza silva-138-99-tax.qza
gg-13-8-99-nb-weighted-classifier.qza ref-seqs.qza silva-138-99-nbseqs-515-classifier806.qza
gg_12_10_otus.tar.gz ref-taxonomy.qza silva-138-99-seqs.qza
gg_13_5_otus.tar.gz rep-seqs.qza silva-138-99-tax-515-806.qza
gg-13-8-99-515-806-nb-classifier.qza rep-seqs.qza.1 silva-138-99-tax.qza
gg-13-8-99-515-806-nb-weighted-classifier.qza sepp-refs-gg-13-8.qza taxonomy.qza
gg-13-8-99-nb-classifier.qza sepp-refs-silva-128.qza taxonomy.qzv
[salexan5@wilog01 ~]$ cp $QIIME_DATA_RESOURCES/85_otus.fasta .
[salexan5@wilog01 ~]$ ls
85_otus.fasta |
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Issues
Bus Error
If within a job a step fails with a bus error, then our first suggestion will be to look at the amount of memory you have/haven’t allocated for you job. From working with users, the majority of the time it is caused by not requested enough memory for the size of data you’re trying to analyze.
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