Background

How to run SPAdes

  • SPAdes parameter considerations

    --careful		tries to reduce number of mismatches and short indels
    --tmp-dir	<dirname>	directory for temporary files
    -t/--threads	<int>		number of threads
    -m/--memory	<int>		RAM limit for SPAdes in Gb (terminates if exceeded) [default 250 (Gb)]
    --sanger	<filename>	file with Sanger reads
    --pacbio	<filename>	file with PacBio reads
    --nanopore	<filename>	file with Nanopore reads
    
  • Example SLURM Job

    #!/bin/bash
    #SBATCH -J spades4.e%j
    #SBATCH -o spades4.o%j
    #SBATCH --mem 1000GB
    #SBATCH -p LM
    #SBATCH -N 1
    #SBATCH -n 40
    #SBATCH -t 48:00:00
    
    source /usr/share/Modules/init/bash
    module load spades/3.11.1
    
    spades.py \
    -k 21,33,55,77,99,127 \
    -t 16 -m 1000 \
    --pacbio /pylon5/mc48o5p/severin/spadesTutorial/00_rawdata/SRR2093876_subreads.fastq.gz \
    --pe1-1 /pylon5/mc48o5p/severin/spadesTutorial/00_rawdata/SRR2093871_1.fastq.gz  \
    --pe1-2 /pylon5/mc48o5p/severin/spadesTutorial/00_rawdata/SRR2093871_2.fastq.gz  \
    --mp1-1 /pylon5/mc48o5p/severin/spadesTutorial/00_rawdata/SRR2093872_1.fastq.gz  \
    --mp1-2 /pylon5/mc48o5p/severin/spadesTutorial/00_rawdata/SRR2093872_2.fastq.gz  \
    --careful \
    -o BT
    

Expected files generated during assembly

SPAdes files output from assembly
K21 K33 K55
K77 K99 assembly_graph.fastg
assembly_graph_with_scaffolds.gfa before_rr.fasta contigs.fasta
contigs.paths corrected dataset.info
input_dataset.yaml misc mismatch_corrector
params.txt scaffolds.fasta scaffolds.paths
spades.log tmp warnings.log

SLURM standard output

  • An example of the output log can be found here: spades.log

Errors

  • Not enough memory

    These two errors are extremely unhelpful for diagnosing the problem. If you get them, try a computer with much higher memory or running spades single threaded (-t 1). Also, I have seen multiple err code message numbers while attempting multithreaded spades on a low memory machine (<256Gb RAM)

    libgomp: Thread creation failed: Resource temporarily unavailable
    
    finished abnormally, err code: 1
    
  • Remove spaces in fastq files

    If you still are running into errors, you may also consider removing spaces in fastq sequence headers as follows.

    gunzip SRR2093871_1.fastq.gz &
    gunzip SRR2093871_2.fastq.gz &
    gunzip SRR2093872_1.fastq.gz &
    gunzip SRR2093872_2.fastq.gz &
    perl -i -pe 's/ /_/g' SRR2093871_1.fastq &
    perl -i -pe 's/ /_/g' SRR2093871_2.fastq &
    perl -i -pe 's/ /_/g' SRR2093872_2.fastq &
    perl -i -pe 's/ /_/g' SRR2093872_1.fastq &
    gzip SRR2093871_1.fastq &
    gzip SRR2093871_2.fastq &
    gzip SRR2093872_1.fastq &
    gzip SRR2093872_2.fastq &
    

Further Reading

Back to the Assembly and Annotation Index page