Attempting an assembly of our geoduck metagenomics HiSeqX data using Megahit (v.1.1.4) on a Mox node.
Assembly was run using default settings.
Assembly coverage was assessed using the following BBmap (v.38.34) scripts:
bbwrap.sh
(alignments)
pileup.sh
(coverage)
SBATCH script is linked here and pasted in full below:
#!/bin/bash ## Job Name #SBATCH --job-name=megahit ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=5-00:00:00 ## Memory per node #SBATCH --mem=500G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=samwhite@uw.edu ## Specify the working directory for this job #SBATCH --workdir=/gscratch/scrubbed/samwhite/outputs/20190102_metagenomics_geo_megahit # Load Python Mox module for Python module availability module load intel-python3_2017 # Load Open MPI module for parallel, multi-node processing module load icc_19-ompi_3.1.2 # SegFault fix? export THREADS_DAEMON_MODEL=1 # Document programs in PATH (primarily for program version ID) date >> system_path.log echo "" >> system_path.log echo "System PATH for $SLURM_JOB_ID" >> system_path.log echo "" >> system_path.log printf "%0.s-" {1..10} >> system_path.log echo ${PATH} | tr : \\n >> system_path.log # variables fastq_dir=/gscratch/srlab/sam/data/metagenomics/P_generosa megahit=/gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit bbmap_dir=/gscratch/srlab/programs/bbmap_38.34 ## Inititalize arrays fastq_array_R1=() fastq_array_R2=() # Create array of fastq R1 files for fastq in ${fastq_dir}/*R1*.gz; do fastq_array_R1+=(${fastq}) done # Create array of fastq R2 files for fastq in ${fastq_dir}/*R2*.gz; do fastq_array_R2+=(${fastq}) done # Create comma-separated list of input files R1_fastq_list=$(IFS=,; echo "${fastq_array_R1[*]}") R2_fastq_list=$(IFS=,; echo "${fastq_array_R2[*]}") # Run Megahit using paired-end reads ${megahit} \ -1 ${R1_fastq_list} \ -2 ${R2_fastq_list} \ --num-cpu-threads 28 # Determine coverage ## Align reads with BBmap BBwrap ${bbmap_dir}/bbwrap.sh \ ref=megahit_out/final.contigs.fa \ in1=${R1_fastq_list} \ in2=${R2_fastq_list} \ out=aln.sam.gz ## Output contig coverage ${bbmap_dir}/pileup.sh \ in=aln.sam.gz \ out=coverage.txt