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10x Genomics
Chromium De Novo Assembly

Output Overview

A Supernova pipeline produces its output in a single pipeline output directory which, by default, is named according to the flowcell serial number for supernova mkfastq (e.g., HAWT7ADXX) and --id name for supernova run. Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical run may look like:

$ cd /home/jdoe/runs
$ supernova run --id=sample345 \
                --description='control subject 4'\
                --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
 
Martian Runtime - v2.3.3
 
Running preflight checks (please wait)...
2016-04-27 16:55:55 [runtime] (ready)           ID.sample345.ASSEMBLER_CS._ASSEMBLER_PREP.SETUP_CHUNKS
2016-04-27 16:55:58 [runtime] (split_complete)  ID.sample345.ASSEMBLER_CS._ASSEMBLER_PREP.SETUP_CHUNKS
2016-04-27 16:55:58 [runtime] (run:local)       ID.sample345.ASSEMBLER_CS._ASSEMBLER_PREP.SETUP_CHUNKS.fork0.chnk0.main
...
2016-04-27 16:59:39 [runtime] (run:local)       ID.sample345.ASSEMBLER_CS._ASSEMBLER_CP.fork0.join
2016-04-27 16:59:42 [runtime] (join_complete)   ID.sample345.ASSEMBLER_CS._ASSEMBLER_CP
 
Outputs:
- assembly: /home/jdoe/runs/sample345/outs/assembly
- summary: /home/jdoe/runs/sample345/outs/summary.csv
- report: /home/jdoe/runs/sample345/outs/report.txt

Pipestance completed successfully! Saving pipestance info to sample345/sample345.mri.tgz

In this case,

The contents of the outs/assembly directory are generally opaque to the user and intended to be used by supernova mkoutput in order to generate FASTA-format output files. See Generating Output for information on this step. Please note that the entire contents of the outs directory should be retained until the desired output is generated.

More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.