ABySS Process Killed
Entering edit mode
13 months ago
asarcillo • 0

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! :)

ABySS genome assembly • 421 views
Entering edit mode

I am now thinking that my PC's 16 Gb RAM is not enough

That is more than likely. See: How does the memory requirements of abyss scale ?


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