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SPRING2 Compression Guide

This guide focuses on archive creation.

Basic Syntax

spring2 -c --R1 <input_R1> [--R2 <input_R2>] [--R3 <input_R3>] \
  [--I1 <input_I1>] [--I2 <input_I2>] -o <output.sp>

Supported Compression Inputs

  • Single-end FASTQ
  • Paired-end FASTQ
  • FASTA inputs
  • Gzipped inputs ending in .gz
  • Grouped lane sets with optional read-3 and index lanes

SPRING2 auto-detects FASTQ versus FASTA and auto-detects gzipped input files.

Common Examples

Single-end:

spring2 -c --R1 reads.fastq -o reads.sp

Paired-end:

spring2 -c --R1 reads_1.fastq --R2 reads_2.fastq -o reads.sp

Gzipped paired-end:

spring2 -c --R1 reads_1.fastq.gz --R2 reads_2.fastq.gz -o reads.sp

Grouped paired-end with indexes:

spring2 -c --R1 R1.fastq.gz --R2 R2.fastq.gz --I1 I1.fastq.gz --I2 I2.fastq.gz -o run.sp

Grouped paired-end with read-3 and indexes:

spring2 -c --R1 R1.fastq.gz --R2 R2.fastq.gz --R3 R3.fastq.gz --I1 I1.fastq.gz --I2 I2.fastq.gz -o run.sp

Grouped Lanes

Grouped archives are created when you pass --R3 and/or --I1 / --I2.

Rules:

  • --R3 requires --R2
  • --I1 currently requires --R2
  • --I2 requires --I1

Grouped archives preserve all provided lanes together and restore them with a single decompression command.

Performance Controls

Threads

Use --threads to control concurrency:

spring2 -c --R1 reads.fastq -o reads.sp --threads 8

The default thread count is min(max(1, hw_threads - 1), 16).

Memory Budget

Use --memory to cap effective worker concurrency based on an approximate memory budget:

spring2 -c --R1 reads.fastq --R2 reads_2.fastq -o reads.sp --memory 8

Set --memory 0 to disable this safety knob.

Compression Level

Use --level 1..9 to change the archive compression level used for gzip-style formatting and the internal scaling used for other streams:

spring2 -c --R1 reads.fastq -o reads.sp --level 9

Notes and Metadata

Attach a custom note with --note:

spring2 -c --R1 reads.fastq -o reads.sp --note "batch=07 replicate=A"

That note is stored in archive metadata and shown by preview mode.

Compression-Time Verification

Add --audit to verify the archive immediately after compression:

spring2 -c --R1 reads.fastq --R2 reads_2.fastq -o reads.sp --audit

This runs a dry-run verification pass after archive creation.

Logging

  • Default: progress bar plus warnings and errors
  • --verbose or --verbose info: informational logs
  • --verbose debug: detailed diagnostics

Example:

spring2 -c --R1 reads.fastq -o reads.sp --verbose debug

See Also