Cannot allocate memory

[zuodabin]

Dear Author, when running the code "biser -o Np.SD -t 50 ./first13_chr.fa --gc-heap 3G --max-error 20 --max-edit-error 10 --kmer-size 21", I encountered the following problem stating that there is insufficient memory allocation. How should I adjust it? My Linux machine has 1TB of RAM.

Running BISER v1.4 on 1 genome(s): first13_chr

0. Hard-masking genomes

0%| | 0/1
100%|████████████████████████████████████████| 1/1
100%|████████████████████████████████████████| 1/1
Hard-masking: 06:40s (single: 06:29s)

1. Putative SD detection

0%| | 0/15
7%|██▋ | 1/15
20%|████████ | 3/15
100%|████████████████████████████████████████| 15/15
Search: 1154:57s (single: 4562:57s)

2. Putative SD alignment
   Total alignments: 266,423,140
   ERROR: [Errno 12] Cannot allocate memory

[zuodabin]

first13_chr.fa Genome size is 2.3Gb

[inumanag]

Hi @zuodabin

1. Is your genome soft-masked? The typical reason for large RAM usage/runtime is the insufficient masking. I'd suggest using RepeatMasker with whole DFAM to do that (might take some time).
2. Try increasing --gc-heap to 8-10G at least.