Hi everyone!
Name is Sam and I'd like to ask for help on my contig assembly using ABySS. I've been trying to assemble a contig from paired sequences using ABySS in WSL. I started with a basic script as follows:
abyss-pe k=21 B=2G name=A1k21 in='A1_1.fastq A1_2.fastq'
Then, the following scripts showed:
dirname: missing operand
Try 'dirname --help' for more information.
ABYSS -k21 -q3 --coverage-hist=coverage.hist -s A1k21-bubbles.fa -o A1k21-1.fa A1_1.fastq A1_2.fastq
ABySS 1.5.2
ABYSS -k21 -q3 --coverage-hist=coverage.hist -s A1k21-bubbles.fa -o A1k21-1.fa A1_1.fastq A1_2.fastq
Reading `A1_1.fastq'...
After at least an hour of running, the process stops with the following error:
make: *** [/home/tawilis/anaconda3/bin/abyss-pe.Makefile:370: A1k21-1.fa] Killed
I first thought that my parameters are incorrect or too high for my PC. So, I repeated this process using higher and lower k and B values. I got the same result.
Then I tried testing my installment using Small Synthetic Data Set from GitHub. It ran smoothly with no errors. I guess that means, my installment is right and the program should run with no problems under WSL.
I am now thinking that my PC's 16 Gb RAM is not enough to run my data set. Anyone has any idea how can I solve this? What should I do next? Thank you very much! :)
That is more than likely. See: How does the memory requirements of abyss scale ?