rrwick
commented
6 years ago You'd have to modify Unicycler's SPAdes call in its source code. These are the relevant lines. It would need --memory 1000 or something like that added on. Alternatively, you could run error correction separately and then run Unicycler with --no_correct.
But why does it need so much memory in the first place?! How big is your read set? How big is the genome you're assembling? Don't forget that Unicycler is really just for bacterial isolates, so if you're trying to assemble a large genome, you'll probably run into lots of other problems beside SPAdes' memory usage.
Ryan
Command line: /usr/local/bin/spades.py -1 /app/data/R1.fastq -2 /app/data/R2.fastq -o /app/data/output/spades_assembly/read_correction --only-error-correction
System information: SPAdes version: 3.12.0 Python version: 2.7.15 OS: Linux-3.10.0-514.10.2.el7.x86_64-x86_64-with-Ubuntu-18.04-bionic
I am getting following error. 0:17:11.642 3G / 18G ERROR K-mer Counting (kmer_data.cpp : 353) The reads contain too many k-mers to fit into available memory. You need approx. 303.601GB of free RAM to assemble your dataset
I tried with default threads, "-t 16" and "-t 32" but same error. The params.txt shows "Memory limit (in Gb): 250".
My linux box has 1 TB memory. How can I pass needed memory params to unicycler or set it somewhere?