Write Consolidated AbXtract Dataset

Takes in an AbXtract dataset and write a dataset of user-defined number of leads per cluster or ROI rank ordered by user preference.

Main Parameters

Parameter Name

Eliminate Sequences That Fall Below Thresholds

Maximum Number of CDR1_1 Liabilities

Maximum Number of CDR1_2 Liabilities

Maximum Number of CDR2_1 Liabilities

Maximum Number of CDR2_2 Liabilities

Maximum Number of CDR3_1 Liabilities

Maximum Number of CDR3_2 Liabilities

Maximum Number of Chain_1 Liabilities Across All CDRs

Maximum Number of Chain_2 Liabilities Across All CDRs

Maximum Number of Full-Length HCDR1-3 and LCDR1-3 Liabilities (PacBio Only).

Maximum Number Sequences Per Cluster

Minimum Count Required for Full-Length Sequence

Minimum Percent Required for Full-Length Sequence

Minimum Log2 Enrichment

Minimum Count Required for Indicated Region of Interest (ROI)

Minimum Percent Required for Indicated Region of Interest (ROI)

Maximum Number of Full-Length Sequences

NGS Picking Strategy

Attempt to Fill the Desired Number of Full-Length Sequences Quota

Rank Sanger Clones First in Population

Write the Automated Top Clones Output to CSV File

Parameter Details

Calculation Parameters

  • 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
  • Eliminate Sequences That Fall Below Thresholds (eliminate_thresholds) type: boolean: If turned ON, will remove sequences that are below or above given threshold. NOTE must be turned ON to remove sequences. If set too high may result in sequences below quota.
    Default: False
  • 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
  • Maximum Number of CDR1_1 Liabilities (max_cdr1_1_liabilities) type: integer: Sets max liability allowed in downstream cdr1_1. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of CDR1_2 Liabilities (max_cdr1_2_liabilities) type: integer: Sets max liability allowed in downstream cdr1_2, ignored if using illumina. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of CDR2_1 Liabilities (max_cdr2_1_liabilities) type: integer: Sets max liability allowed in downstream cdr2_1. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of CDR2_2 Liabilities (max_cdr2_2_liabilities) type: integer: Sets max liability allowed in downstream cdr2_2, ignored if using illumina. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of CDR3_1 Liabilities (max_cdr3_1_liabilities) type: integer: Sets max liability allowed in downstream cdr3_1. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of CDR3_2 Liabilities (max_cdr3_2_liabilities) type: integer: Sets max liability allowed in downstream cdr3_2, ignored if using illumina. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of Chain_1 Liabilities Across All CDRs (max_chain_1_liabilities) type: integer: Sets max liability allowed in downstream cdrs in chain_1. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of Chain_2 Liabilities Across All CDRs (max_chain_2_liabilities) type: integer: Sets max liability allowed in downstream cdrs in chain_2, ignored if using illumina. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number of Full-Length HCDR1-3 and LCDR1-3 Liabilities (PacBio Only). (max_fl_liabilities) type: integer: Sets max liability allowed hcdr1-3 and lcdr1-3, ignored if using illumina. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 10 , Max: 100
  • Maximum Number Sequences Per Cluster (max_seq_per_cluster) type: integer: Indicate the maximum number of unique full-length sequences per given cluster. This value may be exceeded if the ‘Write the Automated Top Clones Output to CSV File’ is turned ON
    Default: 10 , Min: 1, Max: 10000
  • 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
  • Minimum Count Required for Full-Length Sequence (minimum_fl_count) type: integer: Sets minimum count allowed for full-length (illumina: vh or vl), (pacbio: vl+vh). IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 1 , Min: 1
  • Minimum Percent Required for Full-Length Sequence (minimum_fl_percent) type: decimal: Sets minimum percent allowed for full-length (illumina: vh or vl), (pacbio: vl+vh). IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 0.0001 , Min: 1e-18, Max: 100.0
  • Minimum Log2 Enrichment (minimum_log2_enrichment) type: decimal: Sets minimum allowed log2 enrichment value. Only use if log2_enrichment compared a distinct ‘early’ to ‘late’ round population. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: -10 , Min: -1000000, Max: 1000000
  • Minimum Count Required for Indicated Region of Interest (ROI) (minimum_roi_count) type: integer: Sets minimum count allowed for the region of interest (e.g. HCDR3+LCDR3), based on how the dataset was processed. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 2 , Min: 1
  • Minimum Percent Required for Indicated Region of Interest (ROI) (minimum_roi_percent) type: decimal: Sets minimum percent allowed for the region of interest (e.g. HCDR3+LCDR3), based on how the dataset was processed. IMPORTANT: must also turn ON ‘Eliminate Sequences That Fall Below Thresholds’ to remove sequence from population.
    Default: 0.001 , Min: 1e-10, Max: 100.0
  • Maximum Number of Clusters Preferred? (number_of_clusters_to_select_from) type: integer: Indicate the maximum number of clusters that you want to choose from. This value may be exceeded if the ‘Write the Automated Top Clones Output to CSV File’ is turned ON
    Default: 40 , Min: 1, Max: 1000000
  • Maximum Number of Full-Length Sequences (number_of_sequences_total) type: integer: Indicate the maximum number of full-length, non-redundant sequences. This value depends on the total number of non-redundant sequences, maximum # of clusters and the maximum # of sequences per cluster. If the total number is below desired, try adjusting max # of clusters or max number of sequences per cluster. Alternatively, if you want to fill quota with additional sequences per cluster turn on the ‘Attempt to Fulfill the Desired Number of Sequences Quota’ parameter
    Default: 100 , Min: 1, Max: 1000000
  • NGS Picking Strategy (picking_strategy) type: string: Indicate the type of picking strategy.
    Default: Uniform
    Choices: Uniform, Most Abundant
  • Attempt to Fill the Desired Number of Full-Length Sequences Quota (quota_attempt) type: boolean: This will attempt to fulfill the total number of sequences quota if goal of desired number of full-length sequences is not reached by 1) selecting additional clones across lower in rank aross designated clusters followed by 2) selecting the remaining top ranked clones from different clusters by prioritizing top clones. NOTE: if turned on, this is likely to result in a greater number of sequences per cluster and if quota still not met, more clusters then designated in total to reach the desired number of full-length sequences goal
    Default: True
  • Rank Sanger Clones First in Population (rank_sanger) type: boolean: Sanger clones, if present, will be ranked first.
    Default: True
  • 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 Automated Top Clones Output to CSV File (write_to_csv_file) type: boolean: Allows the option to write to CSV after the AbXtract Processing, NGS Only 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