Pool: Merge samples (vertically) from the Relate step

Pool: Input files

Pool input file: Relate/Pool report

You can give any number of Relate report files as inputs for the Pool step. You can also give Pool report files, to pool samples that were themselves made by pooling other samples. See List Input Files for ways to list multiple files.

Note

SEISMIC-RNA will not double-count any of your original samples, even if they appear in multiple report files you are pooling. It will just log a warning if it finds any samples given multiple times.

Relate and Pool reports will be pooled only if they share both

• the top-level output directory, i.e. --out-dir (-o)

• the reference

For each pair of these two attributes, SEISMIC-RNA will produce a pooled sample from all Relate/Pool reports with those attributes. The original Relate/Pool report files will not be deleted or modified; you will merely get a new Pool report file for each pooled sample.

For example, if you ran the command

seismic pool -P {pooled} {out}/sample-1/relate/ref-1 {out}/sample-1/relate/ref-2 {out}/sample-2/relate/ref-1 {out}/sample-1/relate/ref-2

where {out} is the path of your output directory from the Relate step and {pooled} is the name you want to give to each pooled sample, then you would get two new Pool reports representing the pooled samples:

• {out}/{pooled}/relate/ref-1/relate-report.json: made from {out}/sample-1/relate/ref-1/relate-report.json and {out}/sample-2/relate/ref-1/relate-report.json

• {out}/{pooled}/relate/ref-2/relate-report.json: made from {out}/sample-1/relate/ref-2/relate-report.json and {out}/sample-2/relate/ref-2/relate-report.json

To pool all valid combinations of Relate/Pool reports in {out} into samples named {pooled}, you can use the command:

seismic pool -P {pooled} {out}

Pool: Settings

Pool setting: Name of pooled sample

You can choose the name of your pooled sample(s) using --pool (-P). If you omit this option in seismic pool, then it will default to pooled. If you omit this option in seismic wf, then the Pool step will not run.

Pool: Output files

All output files go into the directory {out}/{pooled}/relate/{ref}, where {out} is the output directory, {pooled} is the pooled sample name, and {ref} is the name of the reference.

Pool output file: Pool report

SEISMIC-RNA writes a Pool report file, relate-report.json, that records the names of the samples you pooled. See Pool Report for more information. The file is named relate-report.json not because its contents are identical to those of a Relate report file (they aren’t) but because SEISMIC-RNA can more easily use Relate and Pool report files interchangably when they have the same file names. You can pass both Relate and Pool report files into the Mask and Table steps.

Pool: Troubleshoot and optimize

Pool … got duplicate samples

This warning means that an original (unpooled) sample appeared more than once in the report files you are pooling.

For example, suppose that you pool sample-A and sample-B:

seismic pool -P pool-1 out/sample-A out/sample-B

Then you try to pool sample-A with the pooled sample pool-1:

seismic pool -P pool-2 out/sample-A out/pool-1

This second command will warn that sample-A is duplicated because it appears in both the report files for sample-A and pool-1.

If you get this warning, then you should check your Pool report file to ensure it contains all the samples you want and none that you don’t.

Overwriting … would cause data loss

This error means that you attempted to create a pooled sample with the same name as an existing non-pooled sample while using --force, e.g.

seismic pool --force -P sample-A out

if out/sample-A already exists.

Doing so would overwrite the Relate report for the original, non-pooled sample, making the sample unusable (unless you reran seismic relate on that sample). To prevent data loss, the Pool step refuses to overwrite Relate reports, even with --force.