No output from minimap when generating the index first.

[dosshra]

Hello I am trying to use minimap to align genome assembly to a reference genome. Since the genome is very large, (~10GB) I have split the new genome assembly to 2500 contig files and run it in parallel on HPC. To save the time of indexing, I first built a mmi index. These are the commands I used:

minimap2 -x asm20 -t 3 -d ref.mmi ref.fas
minimap2 -ax asm20 -t 20 ref.mmi contig.fas >contig.sam

This is the log I get:

Mon Mar  1 17:25:18 IST 2021
[WARNING]ESC[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.ESC[0m
[M::main::36.784*0.69] loaded/built the index for 6 target sequence(s)
[M::mm_mapopt_update::42.710*0.73] mid_occ = 1347
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 6
[M::mm_idx_stat::46.892*0.75] distinct minimizers: 210756922 (76.44% are singletons); average occurrences: 3.738; average spacing: 5.689
Mon Mar  1 17:26:12 IST 2021

The contig.sam file is empty. Runing minimap without the indexing step is giving the expected SAM file. Thank you

[lh3]

There should be other messages. It is probably killed by your job scheduler. Increase the memory limit.

[dosshra]

Thank you for the response. I am working on ~10GB reference genome with ~1Mb contigs. I am using 120GB RAM. This configuration works well when I do not do the indexing first.