Everything below assumes the module is loaded, and that you are running from your own project's scratch directory (
module use /dataset/project_2020379/modulefiles
module load lazypipe/3.1
PROJDIR=/scratch/$project_name
mkdir -p $PROJDIR/results && cd $PROJDIR
lazypipe.pl -p main --hostgen Homo_sapiens --anns vi.chain3.env -1 reads_R1.fastq.gz -s mysample -t $SLURM_CPUS_PER_TASK -r $PROJDIR/results -v
Submit this as a batch job rather than running it on a login node — see the
-p main is shorthand for the routine chain of steps (pre,flt,ass,rea,ann1,ann2,rep,sta,pack,clean). Each can also be run on its own, which is how you re-do one stage without repeating the rest. This example uses the small paired end library bundled with the pipeline, data/samples/M15small_R*.fastq.
On Roihu the pipeline sits in the read-only dataset project, so copy the sample reads to your own scratch directory first and work from there:
PROJDIR=/scratch/$project_name
mkdir -p $PROJDIR/data/samples && cd $PROJDIR
cp $LAZYPIPE_INSTALL_DIR/data/samples/M15small_R*.fastq data/samples/
Preprocess reads with fastp:
lazypipe.pl -1 data/samples/M15small_R1.fastq -p pre -t 8 -v
Filter host reads against the Neovison vison genome. It is one of the background filters installed on Roihu, so no download or indexing is needed — just name it:
lazypipe.pl -1 data/samples/M15small_R1.fastq -p flt --hostgen Neovison_vison -t 8 -v
lazypipe.pl --filters lists every host and background genome available to --hostgen. Installing a genome that is not on that list is covered in the
Assemble with Megahit and realign the reads to the assembly:
lazypipe.pl -1 data/samples/M15small_R1.fastq -p ass,rea --ass megahit -t 8 -v
Run a first-round annotation with Minimap2:
lazypipe.pl -1 data/samples/M15small_R1.fastq -p ann1 --ann1 minimap.core_nt.abv -t 8 -v
Chain searches within the first round: map contigs with Minimap2, then pass the contigs with no hits to DIAMOND blastp. Without --append this overwrites existing first-round annotations:
lazypipe.pl -1 data/samples/M15small_R1.fastq -p ann1 --ann1 minimap.core_nt.abv,diamondp.uniref100.abv -t 8 -v
Rather than spelling chains out, name a preset with --anns. The command above is close to corent.vi.env; see
Generate the reports, then statistics, packing and cleanup:
lazypipe.pl -1 data/samples/M15small_R1.fastq -p rep -t 8 -v
lazypipe.pl -1 data/samples/M15small_R1.fastq -p sta,pack,clean -t 8 -v
What each of these produces is described under