I am trying to run velveth with paired-end, fastq files for a de novo genome assembly, but after running ~18 hours (16 CPU, 32 GB RAM) my runs end with just "Killed"
I've tried k-mers from 29 up to 81 (it's compiled for up to 99) and the same thing happens each time. An example of what I enter on the command line:
The program reads both fastq files, then it says it's writing them into roadmap file. After that it starts inputting sequences.
Eventually, it kills. Here are the last few lines from the output:
I'm at a loss for what to do. Does anyone know what might be causing this/what I might do to get around this issue?
I've tried k-mers from 29 up to 81 (it's compiled for up to 99) and the same thing happens each time. An example of what I enter on the command line:
Code:
velveth /home/data/v81 81 -fastq -shortPaired1 '/home/data_home/L008_R1.fastq' -fastq -shortPaired2 '/home/data_home/L008_R2.fastq'
Eventually, it kills. Here are the last few lines from the output:
Code:
[64018.420552] Inputting sequence 83000000 / 130691634 [64104.707519] Inputting sequence 84000000 / 130691634 [64191.472864] Inputting sequence 85000000 / 130691634 [64278.668702] Inputting sequence 86000000 / 130691634 [64366.189098] Inputting sequence 87000000 / 130691634 Killed
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