FastQC MultiQC - A.pulchra WGBS E5 Timeseries

2024
E5
timeseries_molecular
WGBS
Acropora pulchra
FastQC
MultiQC
Author

Sam White

Published

December 31, 2024

INTRO

The notebook entry is part of the coral E5 molecular_timeseries project (GitHub repo). I ran FastQC and MultiQC on the A.pulchra WGBS data received on 20241230 in preparation for a quick Bismark alignment, per Steven’s request (GitHub Issue).

Although I didn’t need to run FastQC or MultiQC, I did so because I used recycled code to download the data. Since FastQC and MultiQC are fast, I just ran the entire R Markdown doc anyway.

The resulting MultiQC Report is here (HTML):

Note

The markdown below was knitted from 00.20-D-Apul-WGBS-reads-FastQC-MultiQC.Rmd (commit e167594).

1 Background

This Rmd file will download raw WGBS FastQs for A.pulchra and evaluate them using FastQC and MultiQC(Ewels et al. 2016).

Additionally, it will rename the files. New naming format will be <colony_id>-<timepoint>. This will make the naming consistent across species, improve sample identification, and improve parsing in downstream analyses.

2 Create a Bash variables file

This allows usage of Bash variables across R Markdown chunks.

{
echo "#### Assign Variables ####"
echo ""

echo "# Data directories"
echo 'export timeseries_dir=/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular'
echo 'export output_dir_top=${timeseries_dir}/D-Apul/output/00.20-D-Apul-WGBS-reads-FastQC-MultiQC'
echo 'export raw_reads_dir=${timeseries_dir}/D-Apul/data/wgbs-raw-fastqs'
echo 'export raw_reads_url="https://owl.fish.washington.edu/nightingales/E5-coral-time-series/30-1067895835/"'
echo ""

echo "# Input files"
echo 'export metadata_file="${timeseries_dir}/M-multi-species/data/e5_DNA_Azenta_metadata.csv"'

echo "# Paths to programs"
echo 'export fastqc=/home/shared/FastQC-0.12.1/fastqc'
echo 'export multiqc=/home/sam/programs/mambaforge/bin/multiqc'
echo ""

echo "# Set FastQ filename patterns"
echo "export fastq_pattern='*.fastq.gz'"
echo "export R1_fastq_pattern='*_R1_*.fastq.gz'"
echo "export R2_fastq_pattern='*_R2_*.fastq.gz'"
echo ""

echo "# Set number of CPUs to use"
echo 'export threads=40'
echo ""


echo "## Inititalize arrays"
echo 'export fastq_array_R1=()'
echo 'export fastq_array_R2=()'
echo 'export raw_fastqs_array=()'
echo 'export R1_names_array=()'
echo 'export R2_names_array=()'
echo ""

echo "# Programs associative array"
echo "declare -A programs_array"
echo "programs_array=("
echo '[fastqc]="${fastqc}" \'
echo '[multiqc]="${multiqc}" \'
echo ")"
echo ""

echo "# Print formatting"
echo 'export line="--------------------------------------------------------"'
echo ""
} > .bashvars

cat .bashvars
#### Assign Variables ####

# Data directories
export timeseries_dir=/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular
export output_dir_top=${timeseries_dir}/D-Apul/output/00.20-D-Apul-WGBS-reads-FastQC-MultiQC
export raw_reads_dir=${timeseries_dir}/D-Apul/data/wgbs-raw-fastqs
export raw_reads_url="https://owl.fish.washington.edu/nightingales/E5-coral-time-series/30-1067895835/"

# Input files
export metadata_file="${timeseries_dir}/M-multi-species/data/e5_DNA_Azenta_metadata.csv"
# Paths to programs
export fastqc=/home/shared/FastQC-0.12.1/fastqc
export multiqc=/home/sam/programs/mambaforge/bin/multiqc

# Set FastQ filename patterns
export fastq_pattern='*.fastq.gz'
export R1_fastq_pattern='*_R1_*.fastq.gz'
export R2_fastq_pattern='*_R2_*.fastq.gz'

# Set number of CPUs to use
export threads=40

## Inititalize arrays
export fastq_array_R1=()
export fastq_array_R2=()
export raw_fastqs_array=()
export R1_names_array=()
export R2_names_array=()

# Programs associative array
declare -A programs_array
programs_array=(
[fastqc]="${fastqc}" \
[multiqc]="${multiqc}" \
)

# Print formatting
export line="--------------------------------------------------------"

3 Download A.pulchra WGBS FastQs

3.1 Inspect metadata file

# Load bash variables into memory
source .bashvars

head ${metadata_file} |
column -t -s","
Sample Name*  Plate         Well number  Azenta sample name  Colony ID  Timepoint  Sample Type*  Species/Strain*  Sample Buffer*    Total Amount (ng)*    Volume (µL)  Conc (ng/µL)  Purification Method*  Biosafety Level (BSL)            Method Used for Fluorescence  Method Used for Spectrophotometry  Method Used for Electrophoresis  
1             41            1            G4                  1G4        ACR-225    TP1           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  2064         80            25.8                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
2             291-20220211  2            A3                  2A3        ACR-225    TP2           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  5064         80            63.3                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
3             527           1            H5                  1H5        ACR-225    TP3           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  4232         80            52.9                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
4             911           1            C6                  1C6        ACR-225    TP4           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  4488         80            56.1                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
5             55            1            B2                  1B2        ACR-229    TP1           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  2432         80            30.4                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
6             295           1            E3                  1E3        ACR-229    TP2           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  2760         80            34.5                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
7             531           1            H3                  1H3        ACR-229    TP3           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  5752         80            71.9                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
8             931           1            F7                  1F7        ACR-229    TP4           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  6008         80            75.1                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"
9             49            1            A1                  1A1        ACR-237    TP1           Genomic DNA      Acropora pulchra  Tris buffer (8.0 pH)  1456         80            18.2                  Column clean-up (Zymo Miniprep)  None                          Qubit                              NA                               1.5% TAE agarose non-denaturing gel  "Please keep methylation libraries   as we may want to sequence more"

3.2 Download raw WGBS reads

Reads are downloaded from https://owl.fish.washington.edu/nightingales/E5-coral-time-series/30-1067895835/

Since sequencing included multiple species, the code will also parse only those that are A.pulchra.

Some filenames are preceeded by <sample_number>-- for some reason. This formatting is limited to only samples in E wells, so the code below uses that aspect to retrieve those samples as well.

The --cut-dirs 3 command cuts the preceding directory structure (i.e. nightingales/E5-coral-time-series/30-1067895835/) so that we just end up with the reads.

# Load bash variables into memory
source .bashvars

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

# Create list of only A.pulchra sample names
# Some samples names are preceded by the Sample Number for some reason,
# so this handles that formatting.
sample_list=$(awk -F"," '$11 == "Acropora pulchra" { if ($9 ~ /E/) { print $8 "--" $9 } else { print $9 } }' ${timeseries_dir}/M-multi-species/data/30-1067895835-WGBS-sample-submission-form.csv \
| sort)

echo ""
echo "${line}"
echo ""
echo "Sample list:"
echo ""
echo "${sample_list}"
echo ""
echo "${line}"
echo ""


# Use printf to format each item for use in wget
formatted_list=$(printf "%s_*," ${sample_list})

# Remove the trailing comma
formatted_list="${formatted_list%,}"

# Output the final wget command
echo ""
echo "${line}"
echo ""
echo "Formatted wget accept list:"
echo ""
echo "wget --accept=\"$formatted_list\""
echo ""
echo "${line}"
echo ""

# Run wget to retrieve FastQs and MD5 files
wget \
--directory-prefix ${raw_reads_dir} \
--recursive \
--no-check-certificate \
--continue \
--cut-dirs 3 \
--no-host-directories \
--no-parent \
--quiet \
--accept=\"$formatted_list\" ${raw_reads_url}

ls -lh "${raw_reads_dir}"
--------------------------------------------------------

Sample list:

10--1E7
1A1
1A10
1A12
1A3
1A5
1A6
1A8
1B1
1B10
1B2
1B4
1B5
1C6
1C8
1C9
1D3
1D7
1D8
1D9
1F1
1F5
1F7
1F9
1G4
1G5
1H11
1H2
1H3
1H5
1H6
1H9
2A3
2C2
2D1
2D2
2G2
2H3
39--2E2
6--1E3

--------------------------------------------------------


--------------------------------------------------------

Formatted wget accept list:

wget --accept="10--1E7_*,1A1_*,1A10_*,1A12_*,1A3_*,1A5_*,1A6_*,1A8_*,1B1_*,1B10_*,1B2_*,1B4_*,1B5_*,1C6_*,1C8_*,1C9_*,1D3_*,1D7_*,1D8_*,1D9_*,1F1_*,1F5_*,1F7_*,1F9_*,1G4_*,1G5_*,1H11_*,1H2_*,1H3_*,1H5_*,1H6_*,1H9_*,2A3_*,2C2_*,2D1_*,2D2_*,2G2_*,2H3_*,39--2E2_*,6--1E3_*"

--------------------------------------------------------

total 213G
-rw-r--r-- 1 sam sam 2.6G Dec 30 07:56 10--1E7_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   60 Dec 30 07:56 10--1E7_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 07:59 10--1E7_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   60 Dec 30 07:59 10--1E7_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 08:22 1A10_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 08:22 1A10_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 08:25 1A10_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 08:25 1A10_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 08:33 1A12_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 08:33 1A12_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 08:35 1A12_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 08:35 1A12_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 08:38 1A1_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 08:38 1A1_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 08:41 1A1_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 08:41 1A1_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.1G Dec 30 08:51 1A3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 08:51 1A3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.1G Dec 30 08:54 1A3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 08:54 1A3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 09:02 1A5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:02 1A5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 09:05 1A5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:05 1A5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 09:07 1A6_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:07 1A6_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.4G Dec 30 09:10 1A6_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:10 1A6_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.4G Dec 30 09:18 1A8_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:18 1A8_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.5G Dec 30 09:21 1A8_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:21 1A8_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.7G Dec 30 09:32 1B10_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 09:32 1B10_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.7G Dec 30 09:35 1B10_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 09:35 1B10_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 09:48 1B1_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:48 1B1_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 09:51 1B1_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:51 1B1_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.4G Dec 30 09:54 1B2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:54 1B2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.4G Dec 30 09:57 1B2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 09:57 1B2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.0G Dec 30 10:05 1B4_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 10:05 1B4_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.0G Dec 30 10:08 1B4_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 10:08 1B4_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 10:10 1B5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 10:10 1B5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 10:13 1B5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 10:13 1B5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 11:15 1C6_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 11:15 1C6_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 11:18 1C6_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 11:18 1C6_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.9G Dec 30 11:26 1C8_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 11:26 1C8_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.9G Dec 30 11:29 1C8_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 11:29 1C8_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 11:31 1C9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 11:31 1C9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 11:34 1C9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 11:34 1C9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 12:00 1D3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:00 1D3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 12:03 1D3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:03 1D3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 12:21 1D7_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:21 1D7_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.4G Dec 30 12:23 1D7_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:23 1D7_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 12:26 1D8_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:26 1D8_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 12:28 1D8_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:28 1D8_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.0G Dec 30 12:31 1D9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:31 1D9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.0G Dec 30 12:34 1D9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:34 1D9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.1G Dec 30 12:51 1F1_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:51 1F1_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.1G Dec 30 12:54 1F1_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 12:54 1F1_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.1G Dec 30 13:10 1F5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 13:10 1F5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.0G Dec 30 13:13 1F5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 13:13 1F5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.4G Dec 30 13:19 1F7_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 13:19 1F7_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.4G Dec 30 13:21 1F7_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 13:21 1F7_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 13:28 1F9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 13:28 1F9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 13:30 1F9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 13:30 1F9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.3G Dec 30 14:01 1G4_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:01 1G4_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.3G Dec 30 14:03 1G4_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:03 1G4_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 14:06 1G5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:06 1G5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 14:09 1G5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:09 1G5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 14:35 1H11_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 14:35 1H11_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.5G Dec 30 14:38 1H11_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   57 Dec 30 14:38 1H11_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.9G Dec 30 14:51 1H2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:51 1H2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.0G Dec 30 14:54 1H2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:54 1H2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 14:56 1H3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:56 1H3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 14:59 1H3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 14:59 1H3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 15:07 1H5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:07 1H5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 15:10 1H5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:10 1H5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 15:13 1H6_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:13 1H6_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 15:16 1H6_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:16 1H6_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.8G Dec 30 15:30 1H9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:30 1H9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 15:33 1H9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:33 1H9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.1G Dec 30 15:45 2A3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:45 2A3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.1G Dec 30 15:47 2A3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 15:47 2A3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 16:11 2C2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 16:11 2C2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.6G Dec 30 16:14 2C2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 16:14 2C2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.3G Dec 30 16:23 2D1_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 16:23 2D1_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.3G Dec 30 16:26 2D1_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 16:26 2D1_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 1.8G Dec 30 16:28 2D2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 16:28 2D2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 1.8G Dec 30 16:30 2D2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 16:30 2D2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 17:00 2G2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 17:00 2G2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.7G Dec 30 17:03 2G2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 17:03 2G2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 1.9G Dec 30 17:22 2H3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 17:22 2H3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 1.9G Dec 30 17:24 2H3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   56 Dec 30 17:24 2H3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.4G Dec 30 17:27 39--2E2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   60 Dec 30 17:27 39--2E2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 2.4G Dec 30 17:30 39--2E2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   60 Dec 30 17:30 39--2E2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.2G Dec 30 17:57 6--1E3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam   59 Dec 30 17:57 6--1E3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 3.2G Dec 30 18:00 6--1E3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam   59 Dec 30 18:00 6--1E3_R2_001.fastq.gz.md5
-rw-rw-r-- 1 sam sam 1.6K Jan  2 11:08 fastq_pairs.txt

3.3 Verify raw read checksums

# Load bash variables into memory
source .bashvars

cd "${raw_reads_dir}"

for file in *.md5
do
  md5sum --check "${file}"
done
./10--1E7_R1_001.fastq.gz: OK
./10--1E7_R2_001.fastq.gz: OK
./1A10_R1_001.fastq.gz: OK
./1A10_R2_001.fastq.gz: OK
./1A12_R1_001.fastq.gz: OK
./1A12_R2_001.fastq.gz: OK
./1A1_R1_001.fastq.gz: OK
./1A1_R2_001.fastq.gz: OK
./1A3_R1_001.fastq.gz: OK
./1A3_R2_001.fastq.gz: OK
./1A5_R1_001.fastq.gz: OK
./1A5_R2_001.fastq.gz: OK
./1A6_R1_001.fastq.gz: OK
./1A6_R2_001.fastq.gz: OK
./1A8_R1_001.fastq.gz: OK
./1A8_R2_001.fastq.gz: OK
./1B10_R1_001.fastq.gz: OK
./1B10_R2_001.fastq.gz: OK
./1B1_R1_001.fastq.gz: OK
./1B1_R2_001.fastq.gz: OK
./1B2_R1_001.fastq.gz: OK
./1B2_R2_001.fastq.gz: OK
./1B4_R1_001.fastq.gz: OK
./1B4_R2_001.fastq.gz: OK
./1B5_R1_001.fastq.gz: OK
./1B5_R2_001.fastq.gz: OK
./1C6_R1_001.fastq.gz: OK
./1C6_R2_001.fastq.gz: OK
./1C8_R1_001.fastq.gz: OK
./1C8_R2_001.fastq.gz: OK
./1C9_R1_001.fastq.gz: OK
./1C9_R2_001.fastq.gz: OK
./1D3_R1_001.fastq.gz: OK
./1D3_R2_001.fastq.gz: OK
./1D7_R1_001.fastq.gz: OK
./1D7_R2_001.fastq.gz: OK
./1D8_R1_001.fastq.gz: OK
./1D8_R2_001.fastq.gz: OK
./1D9_R1_001.fastq.gz: OK
./1D9_R2_001.fastq.gz: OK
./1F1_R1_001.fastq.gz: OK
./1F1_R2_001.fastq.gz: OK
./1F5_R1_001.fastq.gz: OK
./1F5_R2_001.fastq.gz: OK
./1F7_R1_001.fastq.gz: OK
./1F7_R2_001.fastq.gz: OK
./1F9_R1_001.fastq.gz: OK
./1F9_R2_001.fastq.gz: OK
./1G4_R1_001.fastq.gz: OK
./1G4_R2_001.fastq.gz: OK
./1G5_R1_001.fastq.gz: OK
./1G5_R2_001.fastq.gz: OK
./1H11_R1_001.fastq.gz: OK
./1H11_R2_001.fastq.gz: OK
./1H2_R1_001.fastq.gz: OK
./1H2_R2_001.fastq.gz: OK
./1H3_R1_001.fastq.gz: OK
./1H3_R2_001.fastq.gz: OK
./1H5_R1_001.fastq.gz: OK
./1H5_R2_001.fastq.gz: OK
./1H6_R1_001.fastq.gz: OK
./1H6_R2_001.fastq.gz: OK
./1H9_R1_001.fastq.gz: OK
./1H9_R2_001.fastq.gz: OK
./2A3_R1_001.fastq.gz: OK
./2A3_R2_001.fastq.gz: OK
./2C2_R1_001.fastq.gz: OK
./2C2_R2_001.fastq.gz: OK
./2D1_R1_001.fastq.gz: OK
./2D1_R2_001.fastq.gz: OK
./2D2_R1_001.fastq.gz: OK
./2D2_R2_001.fastq.gz: OK
./2G2_R1_001.fastq.gz: OK
./2G2_R2_001.fastq.gz: OK
./2H3_R1_001.fastq.gz: OK
./2H3_R2_001.fastq.gz: OK
./39--2E2_R1_001.fastq.gz: OK
./39--2E2_R2_001.fastq.gz: OK
./6--1E3_R1_001.fastq.gz: OK
./6--1E3_R2_001.fastq.gz: OK

4 Rename FastQs for Project Consistency

New naming format will be <colony_id>-<timepoint>.

Use of a temp file, instead of working directory from the metadata file can avoid potential issues with character/text formatting from the input CSV.

# Load bash variables into memory
source .bashvars

cd "${raw_reads_dir}"

# Create an associative array to store the mapping
declare -A number_to_colony_timepoint

# Create a temporary file to store the mapping
temp_mapping_file=$(mktemp)

# Read the metadata file and populate the temporary file using awk
# Maps Azenta sample name to colony_id and timepoint.
awk -F, 'NR > 1 { print $5, $6 "-" $7 }' "$metadata_file" > "$temp_mapping_file"

# Read the temporary file and populate the associative array
while read -r Number colony_timepoint; do
    number_to_colony_timepoint["$Number"]="$colony_timepoint"
done < "$temp_mapping_file"

# Remove the temporary file
rm "$temp_mapping_file"

# Print the associative array for debugging
echo "Number to colony_id-Timepoint mapping:"
for key in "${!number_to_colony_timepoint[@]}"; do
    echo ""
    echo "$key -> ${number_to_colony_timepoint[$key]}"
    echo ""
done

# Iterate over the FastQ files in the current directory
for fastq_file in *.fastq.gz; do
    # Extract the sample number from the filename
    sample_number=$(echo "$fastq_file" | sed -E 's/^([0-9]+--)?([A-Za-z0-9]+).*/\2/')
    
    # Check if the sample number exists in the associative array
    if [[ -n "${number_to_colony_timepoint[$sample_number]}" ]]; then
        new_sample_name="${number_to_colony_timepoint[$sample_number]}"
        new_filename=$(echo "$fastq_file" | sed -E "s/^([0-9]+--)?$sample_number/$new_sample_name/")
        if [[ "$fastq_file" != "$new_filename" ]]; then
            mv "$fastq_file" "$new_filename"
            echo "Renamed $fastq_file to $new_filename"
        else
            echo "No renaming needed for $fastq_file"
        fi
    else
        echo "Sample number '$sample_number' not found in metadata."
        # Debugging: Print all keys in the associative array with quotes
        echo "Available keys in the associative array:"
        for key in "${!number_to_colony_timepoint[@]}"; do
            echo "'$key'"
        done
    fi
done
Number to colony_id-Timepoint mapping:

1B3 -> SR_1-440-NA


1B2 -> ACR-229-TP1


1B1 -> ACR-150-TP3


1B7 -> POC-40-TP3


1B6 -> POR-245-TP2


1B5 -> ACR-244-TP2


1B4 -> ACR-244-TP4


1B9 -> POR-236-TP2


1B8 -> POR-69-TP1


1D5 -> POC-57-TP1


1D4 -> POC-52-TP3


1C1 -> POC-222-TP3


1C2 -> POR-83-TP4


1D7 -> ACR-186-TP4


1D6 -> POR-245-TP4


1C3 -> POC-53-TP3


1D1 -> POR-216-TP2


1B12 -> POC-219-TP4


1C4 -> POC-201-TP2


1C5 -> POC-52-TP4


1B10 -> ACR-150-TP1


1D3 -> ACR-237-TP4


1C6 -> ACR-225-TP4


1B11 -> POR-69-TP4


1D2 -> POR-260-TP1


1C7 -> POC-53-TP1


1C8 -> ACR-145-TP2


1C9 -> ACR-237-TP3


2C3 -> POR-73-TP1


1D9 -> ACR-139-TP3


2C2 -> ACR-145-TP3


1D8 -> ACR-139-TP4


2C1 -> POR-216-TP1


1E2 -> POC-42-TP3


1E3 -> ACR-229-TP2


1E1 -> POC-259-TP4


1E6 -> POR-83-TP1


1E7 -> ACR-237-TP2


1E4 -> POR-74-TP2


1E5 -> POR-245-TP3


1E11 -> POR-260-TP4


1E10 -> POC-259-TP3


1E8 -> POR-262-TP3


1E9 -> POR-73-TP4


1E12 -> POC-222-TP2


2B1 -> SR_3-440B-NA


2B2 -> POC-40-TP2


2B3 -> POR-262-TP4


2E1 -> POR-74-TP1


2E3 -> POC-255-TP4


2E2 -> ACR-186-TP3


1H1 -> POC-57-TP4


1H3 -> ACR-229-TP3


1H2 -> ACR-173-TP3


2D2 -> ACR-173-TP2


1H5 -> ACR-225-TP3


2D3 -> POC-52-TP1


1H4 -> POC-201-TP1


1H7 -> POC-219-TP1


1F9 -> ACR-265-TP2


1F8 -> POC-53-TP4


2D1 -> ACR-150-TP4


1H6 -> ACR-150-TP2


1H9 -> ACR-173-TP1


1F7 -> ACR-229-TP4


1H8 -> POR-74-TP4


1F6 -> POR-260-TP2


1F5 -> ACR-145-TP4


1F4 -> POC-255-TP1


1F3 -> POR-83-TP3


1D10 -> POR-69-TP2


1D11 -> SR_2-84-NA


1F2 -> POC-57-TP3


1D12 -> POR-73-TP3


1F1 -> ACR-244-TP1


2G3 -> POR-74-TP3


2G2 -> ACR-265-TP1


2G1 -> POR-245-TP1


1G8 -> POC-222-TP1


1G9 -> POR-260-TP3


1G12 -> POC-40-TP1


1G11 -> POR-216-TP3


1G10 -> POR-72-TP3


1G4 -> ACR-225-TP1


1G5 -> ACR-173-TP4


1G6 -> POR-236-TP1


1G7 -> POC-222-TP4


1G1 -> POC-57-TP2


1G2 -> POR-216-TP4


1G3 -> POC-259-TP1


2F1 -> POC-255-TP3


2F2 -> POR-83-TP2


2F3 -> POR-72-TP4


2A1 -> POC-40-TP4


1A11 -> POC-201-TP3


1A10 -> ACR-139-TP1


2A3 -> ACR-225-TP2


2A2 -> POR-72-TP2


1A12 -> ACR-186-TP2


2H2 -> POR-262-TP2


2H3 -> ACR-244-TP3


2H1 -> POC-42-TP1


1H10 -> POC-219-TP2


1A6 -> ACR-265-TP3


1A7 -> POR-262-TP1


1C12 -> POC-52-TP2


1H11 -> ACR-265-TP4


1H12 -> POR-73-TP2


1C11 -> POC-42-TP4


1A4 -> POC-259-TP2


1C10 -> POC-53-TP2


1A5 -> ACR-139-TP2


1A2 -> POC-219-TP3


1A3 -> ACR-145-TP1


1A1 -> ACR-237-TP1


1F12 -> POC-255-TP2


1F10 -> POR-72-TP1


1F11 -> POC-42-TP2


1A8 -> ACR-186-TP1


1A9 -> POR-69-TP3

Renamed 10--1E7_R1_001.fastq.gz to ACR-237-TP2_R1_001.fastq.gz
Renamed 10--1E7_R2_001.fastq.gz to ACR-237-TP2_R2_001.fastq.gz
Renamed 1A10_R1_001.fastq.gz to ACR-139-TP1_R1_001.fastq.gz
Renamed 1A10_R2_001.fastq.gz to ACR-139-TP1_R2_001.fastq.gz
Renamed 1A12_R1_001.fastq.gz to ACR-186-TP2_R1_001.fastq.gz
Renamed 1A12_R2_001.fastq.gz to ACR-186-TP2_R2_001.fastq.gz
Renamed 1A1_R1_001.fastq.gz to ACR-237-TP1_R1_001.fastq.gz
Renamed 1A1_R2_001.fastq.gz to ACR-237-TP1_R2_001.fastq.gz
Renamed 1A3_R1_001.fastq.gz to ACR-145-TP1_R1_001.fastq.gz
Renamed 1A3_R2_001.fastq.gz to ACR-145-TP1_R2_001.fastq.gz
Renamed 1A5_R1_001.fastq.gz to ACR-139-TP2_R1_001.fastq.gz
Renamed 1A5_R2_001.fastq.gz to ACR-139-TP2_R2_001.fastq.gz
Renamed 1A6_R1_001.fastq.gz to ACR-265-TP3_R1_001.fastq.gz
Renamed 1A6_R2_001.fastq.gz to ACR-265-TP3_R2_001.fastq.gz
Renamed 1A8_R1_001.fastq.gz to ACR-186-TP1_R1_001.fastq.gz
Renamed 1A8_R2_001.fastq.gz to ACR-186-TP1_R2_001.fastq.gz
Renamed 1B10_R1_001.fastq.gz to ACR-150-TP1_R1_001.fastq.gz
Renamed 1B10_R2_001.fastq.gz to ACR-150-TP1_R2_001.fastq.gz
Renamed 1B1_R1_001.fastq.gz to ACR-150-TP3_R1_001.fastq.gz
Renamed 1B1_R2_001.fastq.gz to ACR-150-TP3_R2_001.fastq.gz
Renamed 1B2_R1_001.fastq.gz to ACR-229-TP1_R1_001.fastq.gz
Renamed 1B2_R2_001.fastq.gz to ACR-229-TP1_R2_001.fastq.gz
Renamed 1B4_R1_001.fastq.gz to ACR-244-TP4_R1_001.fastq.gz
Renamed 1B4_R2_001.fastq.gz to ACR-244-TP4_R2_001.fastq.gz
Renamed 1B5_R1_001.fastq.gz to ACR-244-TP2_R1_001.fastq.gz
Renamed 1B5_R2_001.fastq.gz to ACR-244-TP2_R2_001.fastq.gz
Renamed 1C6_R1_001.fastq.gz to ACR-225-TP4_R1_001.fastq.gz
Renamed 1C6_R2_001.fastq.gz to ACR-225-TP4_R2_001.fastq.gz
Renamed 1C8_R1_001.fastq.gz to ACR-145-TP2_R1_001.fastq.gz
Renamed 1C8_R2_001.fastq.gz to ACR-145-TP2_R2_001.fastq.gz
Renamed 1C9_R1_001.fastq.gz to ACR-237-TP3_R1_001.fastq.gz
Renamed 1C9_R2_001.fastq.gz to ACR-237-TP3_R2_001.fastq.gz
Renamed 1D3_R1_001.fastq.gz to ACR-237-TP4_R1_001.fastq.gz
Renamed 1D3_R2_001.fastq.gz to ACR-237-TP4_R2_001.fastq.gz
Renamed 1D7_R1_001.fastq.gz to ACR-186-TP4_R1_001.fastq.gz
Renamed 1D7_R2_001.fastq.gz to ACR-186-TP4_R2_001.fastq.gz
Renamed 1D8_R1_001.fastq.gz to ACR-139-TP4_R1_001.fastq.gz
Renamed 1D8_R2_001.fastq.gz to ACR-139-TP4_R2_001.fastq.gz
Renamed 1D9_R1_001.fastq.gz to ACR-139-TP3_R1_001.fastq.gz
Renamed 1D9_R2_001.fastq.gz to ACR-139-TP3_R2_001.fastq.gz
Renamed 1F1_R1_001.fastq.gz to ACR-244-TP1_R1_001.fastq.gz
Renamed 1F1_R2_001.fastq.gz to ACR-244-TP1_R2_001.fastq.gz
Renamed 1F5_R1_001.fastq.gz to ACR-145-TP4_R1_001.fastq.gz
Renamed 1F5_R2_001.fastq.gz to ACR-145-TP4_R2_001.fastq.gz
Renamed 1F7_R1_001.fastq.gz to ACR-229-TP4_R1_001.fastq.gz
Renamed 1F7_R2_001.fastq.gz to ACR-229-TP4_R2_001.fastq.gz
Renamed 1F9_R1_001.fastq.gz to ACR-265-TP2_R1_001.fastq.gz
Renamed 1F9_R2_001.fastq.gz to ACR-265-TP2_R2_001.fastq.gz
Renamed 1G4_R1_001.fastq.gz to ACR-225-TP1_R1_001.fastq.gz
Renamed 1G4_R2_001.fastq.gz to ACR-225-TP1_R2_001.fastq.gz
Renamed 1G5_R1_001.fastq.gz to ACR-173-TP4_R1_001.fastq.gz
Renamed 1G5_R2_001.fastq.gz to ACR-173-TP4_R2_001.fastq.gz
Renamed 1H11_R1_001.fastq.gz to ACR-265-TP4_R1_001.fastq.gz
Renamed 1H11_R2_001.fastq.gz to ACR-265-TP4_R2_001.fastq.gz
Renamed 1H2_R1_001.fastq.gz to ACR-173-TP3_R1_001.fastq.gz
Renamed 1H2_R2_001.fastq.gz to ACR-173-TP3_R2_001.fastq.gz
Renamed 1H3_R1_001.fastq.gz to ACR-229-TP3_R1_001.fastq.gz
Renamed 1H3_R2_001.fastq.gz to ACR-229-TP3_R2_001.fastq.gz
Renamed 1H5_R1_001.fastq.gz to ACR-225-TP3_R1_001.fastq.gz
Renamed 1H5_R2_001.fastq.gz to ACR-225-TP3_R2_001.fastq.gz
Renamed 1H6_R1_001.fastq.gz to ACR-150-TP2_R1_001.fastq.gz
Renamed 1H6_R2_001.fastq.gz to ACR-150-TP2_R2_001.fastq.gz
Renamed 1H9_R1_001.fastq.gz to ACR-173-TP1_R1_001.fastq.gz
Renamed 1H9_R2_001.fastq.gz to ACR-173-TP1_R2_001.fastq.gz
Renamed 2A3_R1_001.fastq.gz to ACR-225-TP2_R1_001.fastq.gz
Renamed 2A3_R2_001.fastq.gz to ACR-225-TP2_R2_001.fastq.gz
Renamed 2C2_R1_001.fastq.gz to ACR-145-TP3_R1_001.fastq.gz
Renamed 2C2_R2_001.fastq.gz to ACR-145-TP3_R2_001.fastq.gz
Renamed 2D1_R1_001.fastq.gz to ACR-150-TP4_R1_001.fastq.gz
Renamed 2D1_R2_001.fastq.gz to ACR-150-TP4_R2_001.fastq.gz
Renamed 2D2_R1_001.fastq.gz to ACR-173-TP2_R1_001.fastq.gz
Renamed 2D2_R2_001.fastq.gz to ACR-173-TP2_R2_001.fastq.gz
Renamed 2G2_R1_001.fastq.gz to ACR-265-TP1_R1_001.fastq.gz
Renamed 2G2_R2_001.fastq.gz to ACR-265-TP1_R2_001.fastq.gz
Renamed 2H3_R1_001.fastq.gz to ACR-244-TP3_R1_001.fastq.gz
Renamed 2H3_R2_001.fastq.gz to ACR-244-TP3_R2_001.fastq.gz
Renamed 39--2E2_R1_001.fastq.gz to ACR-186-TP3_R1_001.fastq.gz
Renamed 39--2E2_R2_001.fastq.gz to ACR-186-TP3_R2_001.fastq.gz
Renamed 6--1E3_R1_001.fastq.gz to ACR-229-TP2_R1_001.fastq.gz
Renamed 6--1E3_R2_001.fastq.gz to ACR-229-TP2_R2_001.fastq.gz

5 FastQC/MultiQC on raw reads

# Load bash variables into memory
source .bashvars

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


# Create array of trimmed FastQs
raw_fastqs_array=(${raw_reads_dir}/${fastq_pattern})

# 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
${programs_array[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 ""

${programs_array[multiqc]} \
${raw_reads_dir} \
--interactive \
-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 ""

# View directory contents
ls -lh ${raw_reads_dir}
Beginning FastQC on raw reads...

application/gzip
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FastQC on raw reads complete!

Beginning MultiQC on raw FastQC...


  /// MultiQC 🔍 | v1.14

|           multiqc | MultiQC Version v1.27 now available!
|           multiqc | Search path : /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/wgbs-raw-fastqs
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 321/321  
|            fastqc | Found 80 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : ../data/wgbs-raw-fastqs/multiqc_report.html
|           multiqc | Data        : ../data/wgbs-raw-fastqs/multiqc_data
|           multiqc | MultiQC complete

MultiQC on raw FastQs complete.

Removing FastQC zip files.

FastQC zip files removed.

total 213G
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References

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.