Entering edit mode
2.7 years ago
ManuelDB
▴
110
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
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