This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Bus error (core dumped) when Aligning contigs to the reference in QUAST

I have 2 paired-end FASTQ files with Illumina reads and I did a de-novo assembly with Spades

 SPAdes-3.15.4-Linux/bin/spades.py \
   -1 W2107026_S1_L001_R1_001.fastq \
   -2 W2107026_S1_L001_R2_001.fastq \
   -o results

Then, with the contigs.fasta I want to run QUAST

 quast contigs.fasta  -r GRCh37_no_gl000201.fa \
    --eukaryote \
    --gene-finding \
    --features ROI.bed \
    -large
    --fragmented

With this, I got

 Running Contig analyzer...
      arge
  Logging to files /results/quast_results/results_2022_03_30_10_02_13/contigs_reports/contigs_report_arge.stdout and contigs_report_arge.stderr...
  Aligning contigs to the reference
Bus error (core dumped)

This is the first time I work with de-novo assemblies so not sure if I am doing something wrong

spades quast

how much memory RAM do you have? I think you need more memory. Have you tried the --memory-efficient option?

I missed that option. I am trying now. I will let you know as soon as the execution finishes

Killed!!

So I need to submit this instead of running it directly in the command line of the terminal

0 answers

No answers yet.

Log in to answer this question.