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JSON output file
This page describes the contents of the gzipped JSON file log.json.gz,
made when running viridian run_one_sample.
The file contains a dictionary of run details. The main entries (keys) are:
-
run_summary- has high-level details on the run -
stages_completed- the progress of each main stage in the pipeline -
reads- high-level summary of read counts -
read_depth- genome coverage and read depth information -
amplicon_scheme_name- name of the identified amplicon scheme -
scheme_choice- details of the amplicon scheme scoring -
amplicons- details of the amplicon scheme that was used -
self_qc- details of read pileup information at each masked position -
sequences- consensus sequence and variations (for MSAs and tree building)
Please read on for more details about the contents of each of those entries.
This section is a dictionary with a basic summary of the run. Here is an example (some key/value pairs are omitted for brevity):
"last_stage_completed": "Finished",
"command": "viridian run_one_sample ... full command line used",
"options:" {
"debug": false,
"outdir": "OUT",
"force": false,
... all the other command line options ...
},
"cwd": "/foo/bar/",
"version": "1.1.0",
"finished_running": true,
"start_time": "2023-09-08T13:37:59+00:00",
"end_time": "2023-09-08T13:39:28+00:00",
"hostname": "thehoff",
"result": "Success",
"errors": [],
"temp_processing_dir": "/tmp/viridian.rxs2ttki",
"total_amplicons": 98,
"successful_amplicons": 98,
"consensus_length": 29836,
"consensus_N_count": 96,
"consensus_N_percent": 0.32,
"consensus_ACGT_count": 29740,
"consensus_ACGT_percent": 99.68,
"consensus_het_count": 0,
"consensus_het_percent": 0.0,
"run_time": "0:01:29.384867"
The most important thing to check is:
"result": "Success"
meaning that the run finished successfully.
If instead is says "Fail", then something went wrong and
the details will be in the stages_completed section.
The other entries should be self-explanatory.
This is a list of the stages that were completed. Each time a stage finishes the json file is written, so that if Viridian crashes or is killed, you can see the last stage that was run.
A successful run looks like this:
"stages_completed": [
"1/10 Start pipeline (0.0s)",
"2/10 Process amplicon scheme files (0.1s)",
"3/10 Map reads to reference (36.8s)",
"4/10 Detect amplicon scheme (2.7s)",
"5/10 Sample reads (23.3s)",
"6/10 Initial consensus sequence (6.1s)",
"7/10 Initial VCF and MSA of consensus/reference (0.4s)",
"8/10 QC using reads vs consensus sequence (17.9s)",
"9/10 Final QC checks (0.1s)",
"10/10 Tidy up final files and log (1.0s)",
"Finished"
]
The entries can vary depending on the command line options. For example, if a BAM file of mapped reads was provided, then the "Map reads to reference" stage would not be present. However, the final entry for a successful run is always "Finished".
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