Enrichment and Relative Abundance Calculation

Calculates the relative fold enrichment from one round of selection (‘early’) to another (‘late’). The number of records in the output is geared to identify the final round in the context of early round, so if values are found in both rounds, only one copy of the given full-length sequence is retained. This is to avoid redundancy in the final output.

Main Parameters

Parameter Name

Correction Factor Group 1

Correction Factor Group 2

Keep Only Functional Sequences

Region to Consider for Enrichment

Minimum Count for the Region of Interest (ROI)

Minimum Percent for the Region of Interest (ROI)

Write the Enrich and Relative Abundance Output to CSV File

Parameter Details

Calculation Parameters

  • Correction Factor Group 1 (correction_factor1) type: integer: Final round values that are not found in earlier rounds are divided by this value, greater means greater weight to clones only found in final round
    Default: 2
  • Correction Factor Group 2 (correction_factor2) type: integer: Early round values that are not found in final round are divided by this value, greater means bigger penalty for de-enrichment
    Default: 10
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • Keep Only Functional Sequences (filter_functional) type: boolean: Eliminates non-functional sequences, truncations, stop-codons, frame-shifts
    Default: True
  • None (floe_report_name) type: string:
    Default: Identify Enriched Populations
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Region to Consider for Enrichment (roi) type: string: Indicate the region of interest that should be considered for the enrichment
    Default: CDR3 Chain 2
    Choices: Merged CDRs, CDR3 Chain 1, CDR3 Chain 2, HCDR3 and LCDR3, Full-Length
  • Minimum Count for the Region of Interest (ROI) (roi_count) type: integer: This will set the minimum count for a given region of interest, all below will be removed.
    Default: 1 , Min: 1, Max: 10000000000
  • Minimum Percent for the Region of Interest (ROI) (roi_percent) type: decimal: This will set the minimum percent for a given region of interest, all below will be removed.
    Default: 1e-12 , Min: 1e-12, Max: 100
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Write the Enrich and Relative Abundance Output to CSV File (write_to_csv_file) type: boolean: Allows the option to write to CSV after the AbXtract Processing file at the cost of additional time. If not, can do this in separate step. Writes to empty file if turned off.
    Default: True

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network