Trimming - Shelly S.salar RNAseq Using fastp and MultiQC on Mox

2020
Miscellaneous
Author

Sam White

Published

October 29, 2020

Shelly asked that I trim, align to a genome, and perform transcriptome alignment counts in this GitHub issue with some Salmo salar RNAseq data she had and, using a subset of the NCBI Salmo salar RefSeq genome, GCF_000233375.1. She created a subset of this genome using only sequences designated as “chromosomes.” A link to the FastA (and a link to her notebook on creating this file) are in that GitHub issue link above. The transcriptome she has provided has not been subsetted in a similar fashion; maybe I’ll do that prior to alignment.

Here, I performed adapter trimming using fastp. I opt for this trimmer as:

I’ll run fastp, followed by MultiQC on Mox.

SBATCH script (GitHub):

#!/bin/bash
## Job Name
#SBATCH --job-name=202001029_ssal_RNAseq_fastp_trimming
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-00:00:00
## Memory per node
#SBATCH --mem=200G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20201029_ssal_RNAseq_fastp_trimming


### S.salar RNAseq trimming using fastp, and MultiQC.

### FastQ files provided by Shelly Trigg. See this GitHub issue for deets:
### https://github.com/RobertsLab/resources/issues/1016#issuecomment-718812876

### Expects input FastQ files to be in format: Pool26_16_P_31_1.fastq.gz



###################################################################################
# These variables need to be set by user

## Assign Variables

# Set number of CPUs to use
threads=27

# Input/output files
trimmed_checksums=trimmed_fastq_checksums.md5
raw_reads_dir=/gscratch/srlab/sam/data/S_salar/RNAseq
fastq_checksums=raw_fastq_checksums.md5

# Paths to programs
fastp=/gscratch/srlab/programs/fastp-0.20.0/fastp
multiqc=/gscratch/srlab/programs/anaconda3/bin/multiqc

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


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


###################################################################################

# Exit script if any command fails
set -e

# Load Python Mox module for Python module availability
module load intel-python3_2017

# Capture date
timestamp=$(date +%Y%m%d)

# Sync raw FastQ files to working directory
rsync --archive --verbose \
"${raw_reads_dir}"*.gz .

# Create arrays of fastq R1 files and sample names
for fastq in *_1.fastq.gz
do
  fastq_array_R1+=("${fastq}")
    R1_names_array+=("$(echo "${fastq}" | awk 'BEGIN {FS = "[._]";OFS = "_"} {print $1, $2, $3, $4, $5}')")
done

# Create array of fastq R2 files
for fastq in *_2.fastq.gz
do
  fastq_array_R2+=("${fastq}")
    R2_names_array+=("$(echo "${fastq}" |awk 'BEGIN {FS = "[._]";OFS = "_"} {print $1, $2, $3, $4, $5}')")
done

# Create list of fastq files used in analysis
# Create MD5 checksum for reference
for fastq in *.gz
do
  echo "${fastq}" >> input.fastq.list.txt
    md5sum >> ${fastq_checksums}
done

# Run fastp on files
# Adds JSON report output for downstream usage by MultiQC
for index in "${!fastq_array_R1[@]}"
do
  R1_sample_name=$(echo "${R1_names_array[index]}")
    R2_sample_name=$(echo "${R2_names_array[index]}")
    ${fastp} \
    --in1 ${fastq_array_R1[index]} \
    --in2 ${fastq_array_R2[index]} \
    --detect_adapter_for_pe \
    --thread ${threads} \
    --html "${R1_sample_name}".fastp-trim."${timestamp}".report.html \
    --json "${R1_sample_name}".fastp-trim."${timestamp}".report.json \
    --out1 "${R1_sample_name}".fastp-trim."${timestamp}".fq.gz \
    --out2 "${R2_sample_name}".fastp-trim."${timestamp}".fq.gz

    # Generate md5 checksums for newly trimmed files
    {
        md5sum "${R1_sample_name}".fastp-trim."${timestamp}".fq.gz
        md5sum "${R2_sample_name}".fastp-trim."${timestamp}".fq.gz
    } >> "${trimmed_checksums}"
    # Remove original FastQ files
    rm "${fastq_array_R1[index]}" "${fastq_array_R2[index]}"
done

# Run MultiQC
${multiqc} .



# Capture program options
for program in "${!programs_array[@]}"
do
    {
  echo "Program options for ${program}: "
    echo ""
    ${programs_array[$program]} -h
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
} &>> program_options.log || true

  # If MultiQC is in programs_array, copy the config file to this directory.
  if [[ "${program}" == "multiqc" ]]; then
    cp --preserve ~/.multiqc_config.yaml "${timestamp}_multiqc_config.yaml"
  fi
done


# Document programs in PATH (primarily for program version ID)
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log

# Remove raw FastQ file
while read -r line
do
    echo ""
    echo "Removing ${line}"
    rm "${line}"
done < input.fastq.list.txt

RESULTS

Cumulative runtime for fastp and MultiQC was very fast; ~18mins:

Cumulative runtime for fastp and MultiQC

NOTE: Despite the “FAILED” indication, the script ran to completion. The last command in the script is a redundant file removal step, which triggered the script “failure”. Left the command in the SBATCH script above for reproducibility.

Overall, the results look good to me. Will proceed with Hisat2 alignment to the custome genome provided by Shelly.

Output folder:

MultiQC Report (HTML; can open link in browser):

  • NOTE: Sample names listed in the report are inaccurate and reflect a filename parsing issue, however, the data/results are fine.

  • multiqc_report.html

Trimmed FastQ files and corresponding fastp HTML reportj: