Supernova2.0, printed on 12/26/2024
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 - 2.3.2 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,
/home/jdoe/runs/ is where the pipeline was run.
/home/jdoe/runs/sample534/ is the pipeline output directory.
/home/jdoe/runs/sample534/outs/ contains the pipeline output files.
/home/jdoe/runs/sample534/outs/summary.csv contains summary metrics.
/home/jdoe/runs/sample534/outs/report.txt contains detailed assembly metrics.
/home/jdoe/runs/sample534/outs/assembly contains all of the assembly files.
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.