metaSPAdes Assembly¶
SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. See the SPAdes home page for more info.
metaSPAdes can be run by the following command:
cd /vol/spool/workdir/assembly/
qsub -cwd -pe multislot 14 -N metaspades -b y \
/usr/local/lib/SPAdes-3.11.1-Linux/bin/metaspades.py -o metaspades_out --pe1-1 read1.fq --pe1-2 read2.fq
The contig sequences are located in the metaspades_out directory in file contigs.fasta. Again, let’s get some basic statistics on the contigs:
getN50.pl -s 500 -f metaspades_out/contigs.fasta
Note
Most jobs above will be started on the compute cluster using the qsub
.
qstat
: check the status and JOBNUMBER of your jobsqdel JOBNUMBER
: delete job with job number JOBNUMBER
We usually submit the jobs to the cluster giving them a job name by using -N JOBNAME
.
This will create log-files named
JOBNAME.oJOBNUMBER
: standard output messages of the toolJOBNAME.eJOBNUMBER
: standard error messages of the tool
You can look into these files by typing e.g. less JOBNAME.oJOBNUMBER
(hit q
to quit)
or tail -f JOBNAME.oJOBNUMBER
(hit ^C
to quit).