Cannot run Alpha Diversity and Alpha Rarefaction

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Marcos Morales

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Jan 22, 2020, 1:48:48 PM1/22/20

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Hello everyone

I'm trying to run the alpha_diversity.py and alpha_rarefaction.py script but I'm not having success. In rarefaction, four new folders has created (alpha_div; alpha_div_collated; alpha_rarefaction_plots and rarefaction) but only the alpha_div_collated folder has txt files (chao1, observed_otus and PD_whole_tree).

Even if I run core_diversity_analyses.py, the error is always the same:

**ERROR RAISED DURING STEP:Removing intermediates files

Command returned exit status:1

Stdout:

Stderr

rm: cannot remove 'Output/arare_max4415//rarefaction': Text file busy

rm: cannot remove 'Output/arare_max4415/alpha_div' Text file busy

Can anybody help me?

Thanks

TonyWalters

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Jan 22, 2020, 1:59:05 PM1/22/20

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Hello Marcos,

Just to give the general disclaimer-it's strongly recommended to upgrade to QIIME2, since QIIME 1 isn't updated any more.
https://qiime2.org/

In this particular case, it looks like errors that happen when using the shared folder in the virtual box:
https://groups.google.com/forum/#!searchin/qiime-forum/%22text$20file$20busy%22%7Csort:date/qiime-forum/4LMpgXtLxn4/C2SnA7NUCgAJ