Cluster Report

Cluster Report: Fields

Name	Data Type
Sample	str
Branches	dict[str, str]
Reference	str
Region	str
Seed for the random number generator	int
Start at this many clusters	int
Stop at this many clusters (0 for no limit)	int
Try all numbers of clusters (Ks), even after finding the best number	bool
Write all numbers of clusters (Ks), rather than only the best number	bool
Remove runs with two clusters more similar than this correlation	float
Remove runs with two clusters that differ by less than this MARCD	float
Remove runs where a cluster differs by more than this ARCD from the ensemble average at any position	float
Remove runs where any cluster’s Gini coefficient exceeds this limit	float
Calculate the jackpotting quotient to find over-represented reads	bool
Confidence level for the jackpotting quotient confidence interval	float
Remove runs whose jackpotting quotient exceeds this limit	float
Maximum number of simulations to compute the jackpotting quotient	int
Skip calculating the jackpotting quotient if the reads × positions exceeds this limit	int
Remove Ks with a log likelihood gap larger than this (0 for no limit)	float
Remove Ks where every run has less than this correlation vs. the best	float
Remove Ks where every run has more than this MARCD vs. the best	float
Run EM (successfully) at least this number of times for each K	int
Run EM (successfully or not) at most this number of times for each K	int
Run EM for at least this many iterations	int
Run EM for at most this many iterations	int
Stop EM when the log likelihood increases by less than this threshold	float
Number of unique reads	int
Whether each number of clusters (K) passed filters	dict[str, bool]
Best number of clusters	int
Numbers of clusters written to batches	list[int]
Number of batches	int
Checksums of batches (SHA-512)	dict[str, list[str]]
Time began	str
Time ended	str
Time taken (minutes)	float
Version of SEISMIC-RNA	str

Cluster Report: Example

{
    "Sample": "sample1",
    "Branches": {
        "align": "",
        "idmut": "",
        "filter": "",
        "cluster": ""
    },
    "Reference": "myref",
    "Region": "full",
    "Seed for the random number generator": 918720378,
    "Start at this many clusters": 1,
    "Stop at this many clusters (0 for no limit)": 2,
    "Try all numbers of clusters (Ks), even after finding the best number": false,
    "Write all numbers of clusters (Ks), rather than only the best number": false,
    "Remove runs with two clusters more similar than this correlation": 0.9,
    "Remove runs with two clusters that differ by less than this MARCD": 0.016,
    "Remove runs where a cluster differs by more than this ARCD from the ensemble average at any position": 0.2,
    "Remove runs where any cluster's Gini coefficient exceeds this limit": 0.667,
    "Calculate the jackpotting quotient to find over-represented reads": true,
    "Confidence level for the jackpotting quotient confidence interval": 0.95,
    "Remove runs whose jackpotting quotient exceeds this limit": 1.1,
    "Maximum number of simulations to compute the jackpotting quotient": 12,
    "Skip calculating the jackpotting quotient if the reads \u00d7 positions exceeds this limit": 268435456,
    "Remove Ks with a log likelihood gap larger than this (0 for no limit)": 0.0,
    "Remove Ks where every run has less than this correlation vs. the best": 0.97,
    "Remove Ks where every run has more than this MARCD vs. the best": 0.008,
    "Run EM (successfully) at least this number of times for each K": 6,
    "Run EM (successfully or not) at most this number of times for each K": 30,
    "Run EM for at least this many iterations": 10,
    "Run EM for at most this many iterations": 500,
    "Stop EM when the log likelihood increases by less than this threshold": 0.37,
    "Number of unique reads": 1713,
    "Whether each number of clusters (K) passed filters": {
        "1": true,
        "2": true
    },
    "Best number of clusters": 1,
    "Numbers of clusters written to batches": [
        1
    ],
    "Number of batches": 1,
    "Checksums of batches (SHA-512)": {
        "cluster": [
            "f18798a185a2b4ab94d96b7a90939a605701d89795fcce7b5a9cd1f5c0106c5f507e91532b82d5129d8b77983200cfbd1c5f97e9d001e07a503393d54f6e4320"
        ]
    },
    "Time began": "2026-05-31 at 12:53:29",
    "Time ended": "2026-05-31 at 12:58:34",
    "Time taken (minutes)": 5.1,
    "Version of SEISMIC-RNA": "0.25.3"
}