What comes first, rep-seqs or table? Is there a way to monitor artifacts?

[Kenneth]

Hi,
I imported 5 fastq files and generated sequence.qzv file containing 4037618 sequences.
I performed quality control using dada2.

I was able to generate table.qza artifact. Job took 24 hrs.
However, no rep-seqs.qza file.

I sent job to bg and then disowned. By running ps I saw that “R” command was running. I’m assuming to generate table.qza qiime uses R? R command was no longer running after table.qza was generated.

My questions are:
What artifacts are produced first, rep-seqs.qza or table.qza? Does it depend on order of command input?
How can I see if rep-seqs.qza is being generated? Is there a process I can monitor using ps command?

Background:
New to QIIME.
New to bioinformatics.

Best,
Ken

[ebolyen (Evan Bolyen)]

Hi @Kenneth,

These are some good questions.

@Kenneth

I sent job to bg and then disowned. By running ps I saw that “R” command was running. I’m assuming to generate table.qza qiime uses R? R command was no longer running after table.qza was generated.

There's actually a middle-step where the output can be transformed into something suitable for the .qza file. So the R process just writes the matrix, and the Python does a little more processing on the other side. Then the framework will convert it.

@Kenneth

What artifacts are produced first, rep-seqs.qza or table.qza? Does it depend on order of command input?

Technically it depends on the output order of the plugin (in this case, table, then rep-seqs).

@Kenneth

How can I see if rep-seqs.qza is being generated? Is there a process I can monitor using ps command?

Not exactly, you should see a Python process humming away as it converts/zips that last output.

Let me know if that makes sense!