Qiime2 stopped working - cache problem

Technical Support
1

Hello!

1. My qiime2-2022.8 build stopped working. I tried to re-run dada2 on some .qza files, but the terminal always gave out


qiime dada2 denoise-single --i-demultiplexed-seqs /Users/administrator/dissertation/demux-paired-end-ngs4.qza --p-trim-left 20 --p-trunc-len 155 --o-representative-sequences rep-seqs-dada2-ngs4-single-reads-homogenised.qza --o-table table-dada2-ngs4-single-reads-homogenised.qza --o-denoising-stats stats-dada2-ngs4-single-reads-homogenised.qza

output:

(1/1) Invalid value for '--i-demultiplexed-seqs':
 /Users/administrator/dissertation/demux-paired-end-ngs4.qza' is not a QIIME
  2 Artifact (.qza)

I then re-installed miniconda3 and qime2-2022.8 from scratch. Still the same problem.

2. If I try to re-run my analyses by scratch (meaning: reimporting data), I get a different mistake.


qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /Users/administrator/homogenous/NGS\ 4 --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-ends-ngs4-homogenous.qza

output:

An unexpected error has occurred:

  Directory '/var/folders/lh/ld9r0p7s3p357m6kcksvv4j00000gp/T/qiime2' already exists without proper permissions '0o41777' set. Current permissions are '0o41757.' This most likely means something other than QIIME 2 created the directory '/var/folders/lh/ld9r0p7s3p357m6kcksvv4j00000gp/T/qiime2' or QIIME 2 failed between creating '/var/folders/lh/ld9r0p7s3p357m6kcksvv4j00000gp/T/qiime2' and setting permissions on it.

See above for debug info.

This is really weird because it all worked perfectly until 7 days ago - I read somehwere it has to do with MacOs cleaning up the cache. But these errors persist even after a clean, new installation of miniconda and Qiime2.
Could you help me localise the error? (I am running qiime on High Sierra 10.13.6, IMac late 2010, Intel 7)

Thanks very much!

P.S.
Everything still work fine on my MacBook Pro 2019 1,4 GHz Quad-Core Intel Core i5)

2

Hi @e_flat_minor !
This is actually an error with the new cache implementation that we are trying out .

We have fixed this issue but your environment seems to be alittle behind our latest patch.

Here are the steps to fix this and then it shouldn't be an issue anymore:

  1. Remove this temp directory. It was created by a version of qiime2 that has sets that wrong permissions. rm -r /var/folders/lh/ld9r0p7s3p357m6kcksvv4j00000gp/T/qiime2
  2. Remove and reinstall your qiime2-2022.8 env.

Then you should be good to go!
Let me know if you have any questions!
:turtle:

3

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