What type of memory does QIIME2 use for processes (distributed vs. shared)? qza to qzv

Technical Support
1

Dear all:

I would like to run QIIME2 and it gives an error message. It might be because of the HPC allocation. Answering this question will help me understand how to run jobs on a shared cluster better and address time allocations, etc. I am going over more material for running jobs on a HPC shared computing resource (many researchers), and it mentions submitting jobs differently depending on job memory allocation:

  1. MPI tasks with distributed memory
    vs.
  2. OpenMP with shared memory.

Which of the above two memory options would be used for converting qza to qzv files such as the below step for demux?

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path all_fastq_files
–source-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path demux-paired-end.qza

Plugin error from demux:

Compressed file ended before the end-of-stream marker was reached

Debug info has been saved to /tmp/qiime2-q2cli-err-kik3isb7.log

Thank you!
Laura

2

An off-topic reply has been merged into an existing topic: How to access error log files in conda environment (HPC cluster) - demux qza to qzv error

Please keep replies on-topic in the future.