Comments (3)
Interestingly enough, both --scaffold-gap-max-size 100000
(100 kbp) and --scaffold-gap-max-size 1000000
(1 Mbp) completed, but 10 kbp exceeded available memory.
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Hmm, --scaffold-gap-max-size
should not affect memory usage (at least significantly). Maybe the memory consumption was at the border line (around 350 Gb) and a little bit exceeded it with 10 kbp threshold while succeeded with higher thresholds.
Anyway, we committed few changes in genome analyzer module, so it should become much less memory consuming than before. Our test on several human assemblies showed max RAM consumption of 130 Gb.
I'll try reducing the number of threads.
Yes, this should always work :) Also note that we have --memory-efficient
option which is even more RAM effective (and slow!) than --threads 1
.
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I increased the memory limit to the max available (380 GB), and it succeeded. It looks like it was right on the cusp. Thanks for the improvements!
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Related Issues (20)
- ERROR! File not found (contigs) running on biocontainers/quast:5.2.0 HOT 4
- MetaQUAST 5.2.0 reference genome "not in list" error when "Summarizing results..."
- metaquast coloring error for > 14 samples
- OSError: [Errno 22]
- Error creating Krona plots in metaquast.py HOT 8
- Version of installed minimap2 differs from its version in the QUAST package (2.24) HOT 1
- Augustus busco not running with a conda install
- ERROR! Skipping S7KLEB_S14_L001_R2_001.fastq.00.0_0.cor.fastq.gz because it contains non-ACGTN characters. HOT 1
- [Errno 30] Read-only file system: '/usr/local/lib/python3.10/dist-packages/quast_libs/bwa/make.log' HOT 2
- Issues with the installation
- Issues about 'quast-download-busco' HOT 2
- minimap2 cannot works correctly in the "Running Contig Analyzer" step
- Error occured while running Busco HOT 2
- No space left on device HOT 5
- Bam files in output HOT 1
- What size of genome fraction can be considered low?
- Issues running quast.
- invalid literal for int() with base 10: 'START_A'
- mapped reads count in reads_report
- License issue
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