NF-CORE Methylseq Thermal Transplant

20211021

Initial analysis of the Porites astreoides WGBS data after first round of sequencing.

Making a new directory

mkdir Thermal_Transplant_WGBS

Location of WGBS files:

/data/putnamlab/KITT/hputnam/20211008_Past_ThermalTransplant_WGBS

Location of reference Porites astreoides genome:

/data/putnamlab/kevin_wong1/Past_Genome/past_filtered_assembly.fasta

Creating methylseq script

nano methylseq.sh

#!/bin/bash
#SBATCH --job-name="methylseq"
#SBATCH -t 120:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --mem=500GB
#SBATCH --account=putnamlab
#SBATCH --export=NONE
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=kevin_wong1@uri.edu
#SBATCH -D /data/putnamlab/kevin_wong1/Thermal_Transplant_WGBS
#SBATCH -p putnamlab
#SBATCH --cpus-per-task=3

# load modules needed

module load Nextflow

# run nextflow methylseq

nextflow run nf-core/methylseq -profile singularity \
--aligner bismark \
--igenomes_ignore \
--fasta /data/putnamlab/kevin_wong1/Past_Genome/past_filtered_assembly.fasta \
--save_reference \
--reads '/data/putnamlab/KITT/hputnam/20211008_Past_ThermalTransplant_WGBS/*_R{1,2}_001.fastq.gz' \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 10 --three_prime_clip_r2 10 \
--non_directional \
--cytosine_report \
--relax_mismatches \
--unmapped \
--outdir WGBS_methylseq \
-name WGBS_methylseq

Running methylseq script

sbatch /data/putnamlab/kevin_wong1/Thermal_Transplant_WGBS/methylseq.sh

  • Started October 21 2021 @ 13:50

I am having errors with versions of Nextflow and the igenome conflicts so I am changing the following:

  • adding the --igenomes_ignore flag
  • updating Nextflow and using methylseq v1.6.1
  • used the --input flag instead of --reads
#!/bin/bash
#SBATCH --job-name="methylseq"
#SBATCH -t 120:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --mem=500GB
#SBATCH --account=putnamlab
#SBATCH --export=NONE
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=kevin_wong1@uri.edu
#SBATCH -D /data/putnamlab/kevin_wong1/Thermal_Transplant_WGBS
#SBATCH -p putnamlab
#SBATCH --cpus-per-task=3

# load modules needed

module load Nextflow/21.03.0

# run nextflow methylseq

nextflow run nf-core/methylseq -profile singularity \
--aligner bismark \
--igenomes_ignore \
--fasta /data/putnamlab/kevin_wong1/Past_Genome/past_filtered_assembly.fasta \
--save_reference \
--input '/data/putnamlab/KITT/hputnam/20211008_Past_ThermalTransplant_WGBS/*_R{1,2}_001.fastq.gz' \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 10 --three_prime_clip_r2 10 \
--non_directional \
--cytosine_report \
--relax_mismatches \
--unmapped \
--outdir WGBS_methylseq \
-name WGBS_methylseq_past_TT_1

Running methylseq script

sbatch /data/putnamlab/kevin_wong1/Thermal_Transplant_WGBS/methylseq.sh

  • Started October 21 2021 @ 15:00
  • Job ID 93817

Resuming methylseq script because it timed out

nano methylseq_resume.sh

#!/bin/bash
#SBATCH --job-name="methylseq"
#SBATCH -t 120:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --mem=500GB
#SBATCH --account=putnamlab
#SBATCH --export=NONE
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=kevin_wong1@uri.edu
#SBATCH -D /data/putnamlab/kevin_wong1/Thermal_Transplant_WGBS
#SBATCH -p putnamlab
#SBATCH --exclusive
#SBATCH --cpus-per-task=3

# load modules needed

module load Nextflow/21.03.0

# run nextflow methylseq

nextflow run nf-core/methylseq -resume \
-profile singularity \
--aligner bismark \
--igenomes_ignore \
--fasta /data/putnamlab/kevin_wong1/Past_Genome/past_filtered_assembly.fasta \
--save_reference \
--input '/data/putnamlab/KITT/hputnam/20211008_Past_ThermalTransplant_WGBS/*_R{1,2}_001.fastq.gz' \
--clip_r1 10 \
--clip_r2 10 \
--three_prime_clip_r1 10 --three_prime_clip_r2 10 \
--non_directional \
--cytosine_report \
--relax_mismatches \
--unmapped \
--outdir WGBS_methylseq

Running methylseq script

sbatch /data/putnamlab/kevin_wong1/Thermal_Transplant_WGBS/methylseq_resume.sh

  • Started October 25 2021 @ 10:54
  • Job ID 94131
Written on October 21, 2021