FastQC MultiQC - Yellow Island eDNA Project

2025
eDNA
Yellow Island
FastQC
MultiQC
project-eDNA-yellow
Author

Sam White

Published

April 18, 2025

INTRO

In preparation for QIIME 2 analysis for project-eDNA-yellow (GitHub repo) project, we needed to run an initial quality check on the eDNA FastQs for this project.

Note

The contents below are from markdown knitted from 00.00-fastqc-multiqc-raw-reads.Rmd (commit fdaa5da).

1 BACKGROUND

This notebook will download raw sequencing reads from https://owl.fish.washington.edu/nightingales/eDNA-yellow_island-2023/ and run an initial quality assessement using FastQC and MultiQC (Ewels et al. 2016).

Inputs:

  • Paired-end FastQs

    • Example filename format: Yell_July18_Site1f_S92_L001_R[12]_001.fastq.gz

Outputs:

  • FastQC HTML files.

  • MultiQC HTML report.

Software requirements:

2 Set R variables

# Data directories
data_dir <- "../data/"
raw_reads_dir <- "../data/raw-fastqs"
raw_reads_url <- "https://owl.fish.washington.edu/nightingales/eDNA-yellow_island-2023/"

# PROGRAMS
fastqc <- "/home/sam/programs/FastQC-0.12.1/fastqc"
multiqc <- "/home/sam/programs/miniforge3/bin/multiqc"

# CPUs
threads <- 4


# Export these as environment variables for bash chunks.
Sys.setenv(
  fastqc = fastqc,
  data_dir = data_dir,
  multiqc = multiqc,
  raw_reads_dir = raw_reads_dir,
  raw_reads_url = raw_reads_url,
  threads = threads
)

3 Download raw FastQs

The --cut-dirs 3 command cuts the preceding directory structure (i.e. nightingales/eDNA-yellow_island-2023/) so that we just end up with the reads.

# Make output directory if it doesn't exist
mkdir --parents "${raw_reads_dir}"

wget \
--directory-prefix "${raw_reads_dir}" \
--recursive \
--no-check-certificate \
--continue \
--cut-dirs 3 \
--no-host-directories \
--no-parent \
--quiet \
--accept "*.fastq.gz,*.md5" \
"${raw_reads_url}"

ls -lh "${raw_reads_dir}"
total 2.8G
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site1aa_S130_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1aa_S130_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site1aa_S130_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1aa_S130_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1a_S83_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1a_S83_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1a_S83_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1a_S83_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  20M Aug 21  2023 Yell_July18_Site1bb_S139_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1bb_S139_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  21M Aug 21  2023 Yell_July18_Site1bb_S139_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1bb_S139_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  21M Aug 21  2023 Yell_July18_Site1b_S84_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1b_S84_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  22M Aug 21  2023 Yell_July18_Site1b_S84_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1b_S84_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site1cc_S140_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1cc_S140_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  46M Aug 21  2023 Yell_July18_Site1cc_S140_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1cc_S140_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site1c_S85_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1c_S85_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  18M Aug 21  2023 Yell_July18_Site1c_S85_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1c_S85_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site1dd_S141_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1dd_S141_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site1dd_S141_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1dd_S141_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1d_S86_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1d_S86_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site1d_S86_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1d_S86_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site1ee_S142_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1ee_S142_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1ee_S142_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site1ee_S142_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 4.0M Aug 21  2023 Yell_July18_Site1e_S91_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1e_S91_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 4.0M Aug 21  2023 Yell_July18_Site1e_S91_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1e_S91_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  34M Aug 21  2023 Yell_July18_Site1f_S92_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1f_S92_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  37M Aug 21  2023 Yell_July18_Site1f_S92_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1f_S92_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site1g_S93_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1g_S93_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site1g_S93_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1g_S93_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 9.2M Aug 21  2023 Yell_July18_Site1h_S94_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1h_S94_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 9.4M Aug 21  2023 Yell_July18_Site1h_S94_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1h_S94_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 1.6M Aug 21  2023 Yell_July18_Site1J_S99_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1J_S99_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 1.4M Aug 21  2023 Yell_July18_Site1J_S99_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site1J_S99_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site1k_S100_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1k_S100_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  16M Aug 21  2023 Yell_July18_Site1k_S100_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1k_S100_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 6.3M Aug 21  2023 Yell_July18_Site1L_S101_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1L_S101_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 6.9M Aug 21  2023 Yell_July18_Site1L_S101_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1L_S101_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1m_S102_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1m_S102_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site1m_S102_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1m_S102_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  32M Aug 21  2023 Yell_July18_Site1n_S103_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1n_S103_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  33M Aug 21  2023 Yell_July18_Site1n_S103_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1n_S103_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1o_S104_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1o_S104_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  29M Aug 21  2023 Yell_July18_Site1o_S104_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1o_S104_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 133M Aug 21  2023 Yell_July18_Site1p_S105_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1p_S105_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 133M Aug 21  2023 Yell_July18_Site1p_S105_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1p_S105_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  18M Aug 21  2023 Yell_July18_Site1q_S106_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1q_S106_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site1q_S106_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1q_S106_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  22M Aug 21  2023 Yell_July18_Site1r_S111_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1r_S111_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1r_S111_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1r_S111_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1s_S112_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1s_S112_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1s_S112_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1s_S112_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site1t_S113_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1t_S113_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1t_S113_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1t_S113_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 6.0M Aug 21  2023 Yell_July18_Site1U_S114_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1U_S114_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 6.3M Aug 21  2023 Yell_July18_Site1U_S114_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1U_S114_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1v_S117_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1v_S117_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site1v_S117_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1v_S117_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  26M Aug 21  2023 Yell_July18_Site1w_S118_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1w_S118_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site1w_S118_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1w_S118_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site1x_S119_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1x_S119_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site1x_S119_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1x_S119_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  21M Aug 21  2023 Yell_July18_Site1y_S120_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1y_S120_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  22M Aug 21  2023 Yell_July18_Site1y_S120_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1y_S120_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site1z_S129_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1z_S129_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site1z_S129_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site1z_S129_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  43M Aug 21  2023 Yell_July18_Site5aa_S132_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5aa_S132_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site5aa_S132_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5aa_S132_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site5a_S87_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5a_S87_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  20M Aug 21  2023 Yell_July18_Site5a_S87_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5a_S87_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  51M Aug 21  2023 Yell_July18_Site5bb_S133_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5bb_S133_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  54M Aug 21  2023 Yell_July18_Site5bb_S133_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5bb_S133_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site5b_S88_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5b_S88_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site5b_S88_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5b_S88_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  56M Aug 21  2023 Yell_July18_Site5cc_S134_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5cc_S134_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  58M Aug 21  2023 Yell_July18_Site5cc_S134_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5cc_S134_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 8.7M Aug 21  2023 Yell_July18_Site5c_S89_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5c_S89_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 8.7M Aug 21  2023 Yell_July18_Site5c_S89_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5c_S89_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site5dd_S135_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5dd_S135_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site5dd_S135_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5dd_S135_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site5d_S90_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5d_S90_R1_001.fastq.gz.md5
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-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5d_S90_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  40M Aug 21  2023 Yell_July18_Site5ee_S136_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5ee_S136_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  42M Aug 21  2023 Yell_July18_Site5ee_S136_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5ee_S136_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  38M Aug 21  2023 Yell_July18_Site5e_S95_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5e_S95_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  41M Aug 21  2023 Yell_July18_Site5e_S95_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5e_S95_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  57M Aug 21  2023 Yell_July18_Site5ff_S137_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5ff_S137_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  60M Aug 21  2023 Yell_July18_Site5ff_S137_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5ff_S137_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 1.5M Aug 21  2023 Yell_July18_Site5f_S96_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5f_S96_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 1.3M Aug 21  2023 Yell_July18_Site5f_S96_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5f_S96_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site5gg_S138_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5gg_S138_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam   20 Aug 21  2023 Yell_July18_Site5gg_S138_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   75 Apr 16 16:16 Yell_July18_Site5gg_S138_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  16M Aug 21  2023 Yell_July18_Site5g_S97_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5g_S97_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site5g_S97_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5g_S97_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  42M Aug 21  2023 Yell_July18_Site5h_S98_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5h_S98_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  45M Aug 21  2023 Yell_July18_Site5h_S98_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   73 Apr 16 16:16 Yell_July18_Site5h_S98_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 8.2K Aug 21  2023 Yell_July18_Site5J_S107_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5J_S107_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 8.6K Aug 21  2023 Yell_July18_Site5J_S107_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5J_S107_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 8.1M Aug 21  2023 Yell_July18_Site5k_S108_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5k_S108_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 9.0M Aug 21  2023 Yell_July18_Site5k_S108_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5k_S108_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site5L_S109_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5L_S109_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  26M Aug 21  2023 Yell_July18_Site5L_S109_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5L_S109_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  15M Aug 21  2023 Yell_July18_Site5m_S110_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5m_S110_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site5m_S110_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5m_S110_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  15M Aug 21  2023 Yell_July18_Site5n_S115_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5n_S115_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  16M Aug 21  2023 Yell_July18_Site5n_S115_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5n_S115_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  16M Aug 21  2023 Yell_July18_Site5o_S116_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5o_S116_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  16M Aug 21  2023 Yell_July18_Site5o_S116_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5o_S116_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site5p_S121_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5p_S121_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  20M Aug 21  2023 Yell_July18_Site5p_S121_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5p_S121_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site5q_S122_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5q_S122_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site5q_S122_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5q_S122_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site5r_S123_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5r_S123_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  26M Aug 21  2023 Yell_July18_Site5r_S123_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5r_S123_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site5s_S124_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5s_S124_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site5s_S124_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5s_S124_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  46M Aug 21  2023 Yell_July18_Site5t_S125_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5t_S125_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  12M Aug 21  2023 Yell_July18_Site5u_S126_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5u_S126_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  13M Aug 21  2023 Yell_July18_Site5u_S126_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5u_S126_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  11M Aug 21  2023 Yell_July18_Site5v_S127_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5v_S127_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  12M Aug 21  2023 Yell_July18_Site5v_S127_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5v_S127_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 1.8K Aug 21  2023 Yell_July18_Site5w_S128_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5w_S128_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 2.0K Aug 21  2023 Yell_July18_Site5w_S128_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5w_S128_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  70M Aug 21  2023 Yell_July18_Site5z_S131_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5z_S131_R1_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam  74M Aug 21  2023 Yell_July18_Site5z_S131_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam   74 Apr 16 16:16 Yell_July18_Site5z_S131_R2_001.fastq.gz.md5

3.1 Verify raw read checksums

Removes MD5 files after check to facilitate downstream directory parsing by QIIME 2.


cd "${raw_reads_dir}"

for md5 in *.md5
do
  md5sum --check "${md5}"
  rm "${md5}"
done
Yell_July18_Site1aa_S130_R1_001.fastq.gz: OK
Yell_July18_Site1aa_S130_R2_001.fastq.gz: OK
Yell_July18_Site1a_S83_R1_001.fastq.gz: OK
Yell_July18_Site1a_S83_R2_001.fastq.gz: OK
Yell_July18_Site1bb_S139_R1_001.fastq.gz: OK
Yell_July18_Site1bb_S139_R2_001.fastq.gz: OK
Yell_July18_Site1b_S84_R1_001.fastq.gz: OK
Yell_July18_Site1b_S84_R2_001.fastq.gz: OK
Yell_July18_Site1cc_S140_R1_001.fastq.gz: OK
Yell_July18_Site1cc_S140_R2_001.fastq.gz: OK
Yell_July18_Site1c_S85_R1_001.fastq.gz: OK
Yell_July18_Site1c_S85_R2_001.fastq.gz: OK
Yell_July18_Site1dd_S141_R1_001.fastq.gz: OK
Yell_July18_Site1dd_S141_R2_001.fastq.gz: OK
Yell_July18_Site1d_S86_R1_001.fastq.gz: OK
Yell_July18_Site1d_S86_R2_001.fastq.gz: OK
Yell_July18_Site1ee_S142_R1_001.fastq.gz: OK
Yell_July18_Site1ee_S142_R2_001.fastq.gz: OK
Yell_July18_Site1e_S91_R1_001.fastq.gz: OK
Yell_July18_Site1e_S91_R2_001.fastq.gz: OK
Yell_July18_Site1f_S92_R1_001.fastq.gz: OK
Yell_July18_Site1f_S92_R2_001.fastq.gz: OK
Yell_July18_Site1g_S93_R1_001.fastq.gz: OK
Yell_July18_Site1g_S93_R2_001.fastq.gz: OK
Yell_July18_Site1h_S94_R1_001.fastq.gz: OK
Yell_July18_Site1h_S94_R2_001.fastq.gz: OK
Yell_July18_Site1J_S99_R1_001.fastq.gz: OK
Yell_July18_Site1J_S99_R2_001.fastq.gz: OK
Yell_July18_Site1k_S100_R1_001.fastq.gz: OK
Yell_July18_Site1k_S100_R2_001.fastq.gz: OK
Yell_July18_Site1L_S101_R1_001.fastq.gz: OK
Yell_July18_Site1L_S101_R2_001.fastq.gz: OK
Yell_July18_Site1m_S102_R1_001.fastq.gz: OK
Yell_July18_Site1m_S102_R2_001.fastq.gz: OK
Yell_July18_Site1n_S103_R1_001.fastq.gz: OK
Yell_July18_Site1n_S103_R2_001.fastq.gz: OK
Yell_July18_Site1o_S104_R1_001.fastq.gz: OK
Yell_July18_Site1o_S104_R2_001.fastq.gz: OK
Yell_July18_Site1p_S105_R1_001.fastq.gz: OK
Yell_July18_Site1p_S105_R2_001.fastq.gz: OK
Yell_July18_Site1q_S106_R1_001.fastq.gz: OK
Yell_July18_Site1q_S106_R2_001.fastq.gz: OK
Yell_July18_Site1r_S111_R1_001.fastq.gz: OK
Yell_July18_Site1r_S111_R2_001.fastq.gz: OK
Yell_July18_Site1s_S112_R1_001.fastq.gz: OK
Yell_July18_Site1s_S112_R2_001.fastq.gz: OK
Yell_July18_Site1t_S113_R1_001.fastq.gz: OK
Yell_July18_Site1t_S113_R2_001.fastq.gz: OK
Yell_July18_Site1U_S114_R1_001.fastq.gz: OK
Yell_July18_Site1U_S114_R2_001.fastq.gz: OK
Yell_July18_Site1v_S117_R1_001.fastq.gz: OK
Yell_July18_Site1v_S117_R2_001.fastq.gz: OK
Yell_July18_Site1w_S118_R1_001.fastq.gz: OK
Yell_July18_Site1w_S118_R2_001.fastq.gz: OK
Yell_July18_Site1x_S119_R1_001.fastq.gz: OK
Yell_July18_Site1x_S119_R2_001.fastq.gz: OK
Yell_July18_Site1y_S120_R1_001.fastq.gz: OK
Yell_July18_Site1y_S120_R2_001.fastq.gz: OK
Yell_July18_Site1z_S129_R1_001.fastq.gz: OK
Yell_July18_Site1z_S129_R2_001.fastq.gz: OK
Yell_July18_Site5aa_S132_R1_001.fastq.gz: OK
Yell_July18_Site5aa_S132_R2_001.fastq.gz: OK
Yell_July18_Site5a_S87_R1_001.fastq.gz: OK
Yell_July18_Site5a_S87_R2_001.fastq.gz: OK
Yell_July18_Site5bb_S133_R1_001.fastq.gz: OK
Yell_July18_Site5bb_S133_R2_001.fastq.gz: OK
Yell_July18_Site5b_S88_R1_001.fastq.gz: OK
Yell_July18_Site5b_S88_R2_001.fastq.gz: OK
Yell_July18_Site5cc_S134_R1_001.fastq.gz: OK
Yell_July18_Site5cc_S134_R2_001.fastq.gz: OK
Yell_July18_Site5c_S89_R1_001.fastq.gz: OK
Yell_July18_Site5c_S89_R2_001.fastq.gz: OK
Yell_July18_Site5dd_S135_R1_001.fastq.gz: OK
Yell_July18_Site5dd_S135_R2_001.fastq.gz: OK
Yell_July18_Site5d_S90_R1_001.fastq.gz: OK
Yell_July18_Site5d_S90_R2_001.fastq.gz: OK
Yell_July18_Site5ee_S136_R1_001.fastq.gz: OK
Yell_July18_Site5ee_S136_R2_001.fastq.gz: OK
Yell_July18_Site5e_S95_R1_001.fastq.gz: OK
Yell_July18_Site5e_S95_R2_001.fastq.gz: OK
Yell_July18_Site5ff_S137_R1_001.fastq.gz: OK
Yell_July18_Site5ff_S137_R2_001.fastq.gz: OK
Yell_July18_Site5f_S96_R1_001.fastq.gz: OK
Yell_July18_Site5f_S96_R2_001.fastq.gz: OK
Yell_July18_Site5gg_S138_R1_001.fastq.gz: OK
Yell_July18_Site5gg_S138_R2_001.fastq.gz: OK
Yell_July18_Site5g_S97_R1_001.fastq.gz: OK
Yell_July18_Site5g_S97_R2_001.fastq.gz: OK
Yell_July18_Site5h_S98_R1_001.fastq.gz: OK
Yell_July18_Site5h_S98_R2_001.fastq.gz: OK
Yell_July18_Site5J_S107_R1_001.fastq.gz: OK
Yell_July18_Site5J_S107_R2_001.fastq.gz: OK
Yell_July18_Site5k_S108_R1_001.fastq.gz: OK
Yell_July18_Site5k_S108_R2_001.fastq.gz: OK
Yell_July18_Site5L_S109_R1_001.fastq.gz: OK
Yell_July18_Site5L_S109_R2_001.fastq.gz: OK
Yell_July18_Site5m_S110_R1_001.fastq.gz: OK
Yell_July18_Site5m_S110_R2_001.fastq.gz: OK
Yell_July18_Site5n_S115_R1_001.fastq.gz: OK
Yell_July18_Site5n_S115_R2_001.fastq.gz: OK
Yell_July18_Site5o_S116_R1_001.fastq.gz: OK
Yell_July18_Site5o_S116_R2_001.fastq.gz: OK
Yell_July18_Site5p_S121_R1_001.fastq.gz: OK
Yell_July18_Site5p_S121_R2_001.fastq.gz: OK
Yell_July18_Site5q_S122_R1_001.fastq.gz: OK
Yell_July18_Site5q_S122_R2_001.fastq.gz: OK
Yell_July18_Site5r_S123_R1_001.fastq.gz: OK
Yell_July18_Site5r_S123_R2_001.fastq.gz: OK
Yell_July18_Site5s_S124_R1_001.fastq.gz: OK
Yell_July18_Site5s_S124_R2_001.fastq.gz: OK
Yell_July18_Site5t_S125_R1_001.fastq.gz: OK
Yell_July18_Site5u_S126_R1_001.fastq.gz: OK
Yell_July18_Site5u_S126_R2_001.fastq.gz: OK
Yell_July18_Site5v_S127_R1_001.fastq.gz: OK
Yell_July18_Site5v_S127_R2_001.fastq.gz: OK
Yell_July18_Site5w_S128_R1_001.fastq.gz: OK
Yell_July18_Site5w_S128_R2_001.fastq.gz: OK
Yell_July18_Site5z_S131_R1_001.fastq.gz: OK
Yell_July18_Site5z_S131_R2_001.fastq.gz: OK

4 FastQC/MultiQC on raw reads


# Make output directory if it doesn't exist
mkdir --parents "${raw_reads_dir}"


############ RUN FASTQC ############


# Create array of trimmed FastQs
# Access the individual FastQ files from the array
IFS=' ' read -r -a raw_fastqs_array <<< "${raw_fastqs_string}"

# Pass array contents to new variable as space-delimited list
raw_fastqc_list=$(echo "${raw_fastqs_array[*]}")


echo "Beginning FastQC on raw reads..."
echo ""

# Run FastQC
### NOTE: Do NOT quote raw_fastqc_list
${fastqc} \
--threads ${threads} \
--outdir ${raw_reads_dir} \
--quiet \
${raw_fastqc_list}

echo "FastQC on raw reads complete!"
echo ""

############ END FASTQC ############

############ RUN MULTIQC ############
echo "Beginning MultiQC on raw FastQC..."
echo ""

${multiqc} --interactive \
${raw_reads_dir} \
-o ${raw_reads_dir}

echo ""
echo "MultiQC on raw FastQs complete."
echo ""

############ END MULTIQC ############

echo "Removing FastQC zip files."
echo ""
rm ${raw_reads_dir}/*.zip
echo "FastQC zip files removed."
echo ""
Beginning FastQC on raw reads...

application/gzip
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application/gzip
FastQC on raw reads complete!

Beginning MultiQC on raw FastQC...


/// MultiQC 🔍 v1.28

       file_search | Search path: /home/sam/gitrepos/RobertsLab/project-eDNA-yellow/data/raw-fastqs

            fastqc | Found 119 reports
            fastqc | Sample had zero reads: 'Yell_July18_Site1x_S119_R2_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site5dd_S135_R1_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site5gg_S138_R2_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site5d_S90_R1_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site1aa_S130_R1_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site1aa_S130_R2_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site5gg_S138_R1_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site5dd_S135_R2_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site1x_S119_R1_001'
            fastqc | Sample had zero reads: 'Yell_July18_Site5d_S90_R2_001'

     write_results | Data        : /home/sam/gitrepos/RobertsLab/project-eDNA-yellow/data/raw-fastqs/multiqc_data
     write_results | Report      : /home/sam/gitrepos/RobertsLab/project-eDNA-yellow/data/raw-fastqs/multiqc_report.html
           multiqc | MultiQC complete

MultiQC on raw FastQs complete.

Removing FastQC zip files.

FastQC zip files removed.

5 Check for empty/mismatched FastQs

5.1 Delete empty FastQs

# Path to the fastqc_sequence_counts_plot.txt file
counts_file <- file.path(Sys.getenv("raw_reads_dir"), "multiqc_data", "fastqc_sequence_counts_plot.txt")

# Check if the file exists
if (file.exists(counts_file)) {
  # Read the file
  counts_data <- read.table(counts_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE)

  # Identify samples with Unique Reads equal to 0.0
  zero_reads_samples <- counts_data$Sample[counts_data$Unique.Reads == 0.0]

  # Check if any samples with zero reads were found
  if (length(zero_reads_samples) > 0) {
    cat("FastQ files with zero unique reads found:\n")

    # Loop through the samples and delete the corresponding FastQ files
    for (sample in zero_reads_samples) {
      # Construct the file path
      fastq_file <- file.path(Sys.getenv("raw_reads_dir"), paste0(sample, ".fastq.gz"))

      # Check if the file exists
      if (file.exists(fastq_file)) {
        # Delete the file
        unlink(fastq_file)
        cat("Deleted:", fastq_file, "\n")
      } else {
        cat("File not found:", fastq_file, "\n")
      }
    }
  } else {
    cat("No FastQ files with zero unique reads found.\n")
  }
} else {
  cat("Error: fastqc_sequence_counts_plot.txt file not found at", counts_file, "\n")
}
FastQ files with zero unique reads found:
Deleted: ../data/raw-fastqs/Yell_July18_Site1aa_S130_R1_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site1aa_S130_R2_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site1x_S119_R1_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site1x_S119_R2_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site5d_S90_R1_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site5d_S90_R2_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site5dd_S135_R1_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site5dd_S135_R2_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site5gg_S138_R1_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site5gg_S138_R2_001.fastq.gz

5.2 Check for missing FastQ pairs

# Create the fastq list and string
raw_fastqs_list <- list.files(path = Sys.getenv("raw_reads_dir"), pattern = "\\.fastq\\.gz$", full.names = TRUE)
raw_fastqs_string <- paste(raw_fastqs_list, collapse = " ")

# Update the environment variable with the actual string
Sys.setenv(raw_fastqs_string = raw_fastqs_string)

# Check for matching R1 and R2 files
r1_files <- grep("_R1_", raw_fastqs_list, value = TRUE)
r2_files <- grep("_R2_", raw_fastqs_list, value = TRUE)

# Extract sample names from R1 and R2 files
r1_samples <- gsub("_R1_.*", "", basename(r1_files))
r2_samples <- gsub("_R2_.*", "", basename(r2_files))

# Find unmatched R1 files
unmatched_r1 <- setdiff(r1_samples, r2_samples)
if (length(unmatched_r1) > 0) {
  cat("Unmatched R1 files:\n")
  for (sample in unmatched_r1) {
    r1_file <- grep(paste0("^", sample, "_R1_"), basename(r1_files), value = TRUE)
    r1_file_path <- file.path(Sys.getenv("raw_reads_dir"), r1_file)
    cat(r1_file, "\n")
    # Delete unmatched R1 file
    unlink(r1_file_path)
    cat("Deleted:", r1_file_path, "\n")
  }
}
Unmatched R1 files:
Yell_July18_Site5t_S125_R1_001.fastq.gz 
Deleted: ../data/raw-fastqs/Yell_July18_Site5t_S125_R1_001.fastq.gz 
# Find unmatched R2 files
unmatched_r2 <- setdiff(r2_samples, r1_samples)
if (length(unmatched_r2) > 0) {
  cat("Unmatched R2 files:\n")
  for (sample in unmatched_r2) {
    r2_file <- grep(paste0("^", sample, "_R2_"), basename(r2_files), value = TRUE)
    r2_file_path <- file.path(Sys.getenv("raw_reads_dir"), r2_file)
    cat(r2_file, "\n")
    # Delete unmatched R2 file
    unlink(r2_file_path)
    cat("Deleted:", r2_file_path, "\n")
  }
}

# View directory contents
ls -lh ${raw_reads_dir}
total 2.9G
drwxrwxr-x 2 sam sam 4.0K Apr 18 07:20 multiqc_data
-rw-rw-r-- 1 sam sam 7.0M Apr 18 07:20 multiqc_report.html
-rw-rw-r-- 1 sam sam 186K Apr 18 07:17 Yell_July18_Site1aa_S130_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 186K Apr 18 07:17 Yell_July18_Site1aa_S130_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 875K Apr 18 07:17 Yell_July18_Site1a_S83_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1a_S83_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 888K Apr 18 07:17 Yell_July18_Site1a_S83_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1a_S83_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 860K Apr 18 07:17 Yell_July18_Site1bb_S139_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  20M Aug 21  2023 Yell_July18_Site1bb_S139_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 880K Apr 18 07:17 Yell_July18_Site1bb_S139_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  21M Aug 21  2023 Yell_July18_Site1bb_S139_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 853K Apr 18 07:17 Yell_July18_Site1b_S84_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  21M Aug 21  2023 Yell_July18_Site1b_S84_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 875K Apr 18 07:17 Yell_July18_Site1b_S84_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  22M Aug 21  2023 Yell_July18_Site1b_S84_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 846K Apr 18 07:18 Yell_July18_Site1cc_S140_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site1cc_S140_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 879K Apr 18 07:18 Yell_July18_Site1cc_S140_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  46M Aug 21  2023 Yell_July18_Site1cc_S140_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 873K Apr 18 07:17 Yell_July18_Site1c_S85_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site1c_S85_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 885K Apr 18 07:17 Yell_July18_Site1c_S85_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  18M Aug 21  2023 Yell_July18_Site1c_S85_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 855K Apr 18 07:18 Yell_July18_Site1dd_S141_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site1dd_S141_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 883K Apr 18 07:18 Yell_July18_Site1dd_S141_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site1dd_S141_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 857K Apr 18 07:18 Yell_July18_Site1d_S86_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1d_S86_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 877K Apr 18 07:18 Yell_July18_Site1d_S86_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site1d_S86_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 865K Apr 18 07:18 Yell_July18_Site1ee_S142_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site1ee_S142_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 890K Apr 18 07:18 Yell_July18_Site1ee_S142_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1ee_S142_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 859K Apr 18 07:18 Yell_July18_Site1e_S91_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 4.0M Aug 21  2023 Yell_July18_Site1e_S91_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 882K Apr 18 07:18 Yell_July18_Site1e_S91_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 4.0M Aug 21  2023 Yell_July18_Site1e_S91_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 871K Apr 18 07:18 Yell_July18_Site1f_S92_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  34M Aug 21  2023 Yell_July18_Site1f_S92_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 895K Apr 18 07:18 Yell_July18_Site1f_S92_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  37M Aug 21  2023 Yell_July18_Site1f_S92_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 842K Apr 18 07:18 Yell_July18_Site1g_S93_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site1g_S93_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 873K Apr 18 07:18 Yell_July18_Site1g_S93_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site1g_S93_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 877K Apr 18 07:18 Yell_July18_Site1h_S94_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 9.2M Aug 21  2023 Yell_July18_Site1h_S94_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 883K Apr 18 07:18 Yell_July18_Site1h_S94_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 9.4M Aug 21  2023 Yell_July18_Site1h_S94_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 903K Apr 18 07:18 Yell_July18_Site1J_S99_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 1.6M Aug 21  2023 Yell_July18_Site1J_S99_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 938K Apr 18 07:18 Yell_July18_Site1J_S99_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 1.4M Aug 21  2023 Yell_July18_Site1J_S99_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 863K Apr 18 07:18 Yell_July18_Site1k_S100_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site1k_S100_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 877K Apr 18 07:18 Yell_July18_Site1k_S100_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  16M Aug 21  2023 Yell_July18_Site1k_S100_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 862K Apr 18 07:18 Yell_July18_Site1L_S101_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 6.3M Aug 21  2023 Yell_July18_Site1L_S101_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 884K Apr 18 07:18 Yell_July18_Site1L_S101_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 6.9M Aug 21  2023 Yell_July18_Site1L_S101_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 859K Apr 18 07:18 Yell_July18_Site1m_S102_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1m_S102_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 870K Apr 18 07:18 Yell_July18_Site1m_S102_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  24M Aug 21  2023 Yell_July18_Site1m_S102_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 849K Apr 18 07:18 Yell_July18_Site1n_S103_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  32M Aug 21  2023 Yell_July18_Site1n_S103_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 872K Apr 18 07:18 Yell_July18_Site1n_S103_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  33M Aug 21  2023 Yell_July18_Site1n_S103_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 853K Apr 18 07:18 Yell_July18_Site1o_S104_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1o_S104_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 868K Apr 18 07:18 Yell_July18_Site1o_S104_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  29M Aug 21  2023 Yell_July18_Site1o_S104_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 844K Apr 18 07:18 Yell_July18_Site1p_S105_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 133M Aug 21  2023 Yell_July18_Site1p_S105_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 876K Apr 18 07:18 Yell_July18_Site1p_S105_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 133M Aug 21  2023 Yell_July18_Site1p_S105_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 913K Apr 18 07:18 Yell_July18_Site1q_S106_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  18M Aug 21  2023 Yell_July18_Site1q_S106_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 916K Apr 18 07:18 Yell_July18_Site1q_S106_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site1q_S106_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 870K Apr 18 07:18 Yell_July18_Site1r_S111_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  22M Aug 21  2023 Yell_July18_Site1r_S111_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 882K Apr 18 07:18 Yell_July18_Site1r_S111_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1r_S111_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 851K Apr 18 07:18 Yell_July18_Site1s_S112_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1s_S112_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 861K Apr 18 07:18 Yell_July18_Site1s_S112_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1s_S112_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 855K Apr 18 07:18 Yell_July18_Site1t_S113_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site1t_S113_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 873K Apr 18 07:18 Yell_July18_Site1t_S113_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  28M Aug 21  2023 Yell_July18_Site1t_S113_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 870K Apr 18 07:18 Yell_July18_Site1U_S114_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 6.0M Aug 21  2023 Yell_July18_Site1U_S114_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 905K Apr 18 07:18 Yell_July18_Site1U_S114_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 6.3M Aug 21  2023 Yell_July18_Site1U_S114_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 859K Apr 18 07:18 Yell_July18_Site1v_S117_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  23M Aug 21  2023 Yell_July18_Site1v_S117_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 881K Apr 18 07:18 Yell_July18_Site1v_S117_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site1v_S117_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 870K Apr 18 07:18 Yell_July18_Site1w_S118_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  26M Aug 21  2023 Yell_July18_Site1w_S118_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 885K Apr 18 07:18 Yell_July18_Site1w_S118_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site1w_S118_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 186K Apr 18 07:18 Yell_July18_Site1x_S119_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 186K Apr 18 07:18 Yell_July18_Site1x_S119_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 859K Apr 18 07:18 Yell_July18_Site1y_S120_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  21M Aug 21  2023 Yell_July18_Site1y_S120_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 886K Apr 18 07:18 Yell_July18_Site1y_S120_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  22M Aug 21  2023 Yell_July18_Site1y_S120_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 860K Apr 18 07:18 Yell_July18_Site1z_S129_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site1z_S129_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 887K Apr 18 07:18 Yell_July18_Site1z_S129_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  19M Aug 21  2023 Yell_July18_Site1z_S129_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 863K Apr 18 07:19 Yell_July18_Site5aa_S132_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  43M Aug 21  2023 Yell_July18_Site5aa_S132_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 884K Apr 18 07:19 Yell_July18_Site5aa_S132_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  44M Aug 21  2023 Yell_July18_Site5aa_S132_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 889K Apr 18 07:19 Yell_July18_Site5a_S87_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site5a_S87_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 909K Apr 18 07:19 Yell_July18_Site5a_S87_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  20M Aug 21  2023 Yell_July18_Site5a_S87_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 857K Apr 18 07:19 Yell_July18_Site5bb_S133_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  51M Aug 21  2023 Yell_July18_Site5bb_S133_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 883K Apr 18 07:19 Yell_July18_Site5bb_S133_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  54M Aug 21  2023 Yell_July18_Site5bb_S133_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 852K Apr 18 07:19 Yell_July18_Site5b_S88_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  25M Aug 21  2023 Yell_July18_Site5b_S88_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 877K Apr 18 07:19 Yell_July18_Site5b_S88_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  27M Aug 21  2023 Yell_July18_Site5b_S88_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 853K Apr 18 07:19 Yell_July18_Site5cc_S134_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  56M Aug 21  2023 Yell_July18_Site5cc_S134_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 877K Apr 18 07:19 Yell_July18_Site5cc_S134_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  58M Aug 21  2023 Yell_July18_Site5cc_S134_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 870K Apr 18 07:19 Yell_July18_Site5c_S89_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 8.7M Aug 21  2023 Yell_July18_Site5c_S89_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 875K Apr 18 07:19 Yell_July18_Site5c_S89_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 8.7M Aug 21  2023 Yell_July18_Site5c_S89_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 186K Apr 18 07:19 Yell_July18_Site5dd_S135_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 186K Apr 18 07:19 Yell_July18_Site5dd_S135_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 186K Apr 18 07:19 Yell_July18_Site5d_S90_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 186K Apr 18 07:19 Yell_July18_Site5d_S90_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 871K Apr 18 07:19 Yell_July18_Site5ee_S136_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  40M Aug 21  2023 Yell_July18_Site5ee_S136_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 898K Apr 18 07:19 Yell_July18_Site5ee_S136_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  42M Aug 21  2023 Yell_July18_Site5ee_S136_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 869K Apr 18 07:19 Yell_July18_Site5e_S95_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  38M Aug 21  2023 Yell_July18_Site5e_S95_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 893K Apr 18 07:19 Yell_July18_Site5e_S95_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  41M Aug 21  2023 Yell_July18_Site5e_S95_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 850K Apr 18 07:19 Yell_July18_Site5ff_S137_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  57M Aug 21  2023 Yell_July18_Site5ff_S137_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 874K Apr 18 07:19 Yell_July18_Site5ff_S137_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  60M Aug 21  2023 Yell_July18_Site5ff_S137_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 871K Apr 18 07:19 Yell_July18_Site5f_S96_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 1.5M Aug 21  2023 Yell_July18_Site5f_S96_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 868K Apr 18 07:19 Yell_July18_Site5f_S96_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 1.3M Aug 21  2023 Yell_July18_Site5f_S96_R2_001.fastq.gz
-rw-rw-r-- 1 sam sam 186K Apr 18 07:19 Yell_July18_Site5gg_S138_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam 186K Apr 18 07:19 Yell_July18_Site5gg_S138_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam 914K Apr 18 07:19 Yell_July18_Site5g_S97_R1_001_fastqc.html
-rw-rw-r-- 1 sam sam  16M Aug 21  2023 Yell_July18_Site5g_S97_R1_001.fastq.gz
-rw-rw-r-- 1 sam sam 951K Apr 18 07:19 Yell_July18_Site5g_S97_R2_001_fastqc.html
-rw-rw-r-- 1 sam sam  17M Aug 21  2023 Yell_July18_Site5g_S97_R2_001.fastq.gz
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Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics 32 (19): 3047–48. https://doi.org/10.1093/bioinformatics/btw354.