I'm using abyss 2.0 to assemble a large genome (~1.5 GB). I'm running abyss-pe, but the process dies when the "AdjList" command is launched. I'm pretty sure it's a memory issue because my ".fa" file is too big (8.3G), but not sure how to solve it? Please help!!!
Here's the command that causes trouble:
AdjList -v -k99 -m50 --dot results/assembly_k99_np12_24Gram_B3G_H3_1Gseq-1.fa >results/assembly_k99_np12_24Gram_B3G_H3_1Gseq-1.dot
and the error message:
Finding overlaps of fewer than k-1 bp... terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc /bin/bash: line 1: 32487 Aborted AdjList -v -k99 -m50 --dot results/assembly_k99_np12_24Gram_B3G_H3_1Gseq-1.fa > results/assembly_k99_np12_24Gram_B3G_H3_ make: *** [results/assembly_k99_np12_24Gram_B3G_H3_1Gseq-1.dot] Error 134 make: *** Deleting file `results/assembly_k99_np12_24Gram_B3G_H3_1Gseq-1.dot'