Hi Heng,
I have noticed an issue when I tried to use -junc-bed to improve small exon alignments.
I noticed when I run minimap2 -ax splice -I 1000G -t $num_cores --junc-bed anno.bed $genome $raw_reads > test.sam Even the anno.bed file is not present in the current folder, the command still runs without any issue. I think it will be ignored in the default map-ont mode, but not in splice mode.
[M::mm_idx_gen::69.718*1.52] collected minimizers
[M::mm_idx_gen::148.442*1.66] sorted minimizers
[M::main::148.442*1.66] loaded/built the index for 1566 target sequence(s)
[M::mm_mapopt_update::151.000*1.65] mid_occ = 4082
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 1566
[M::mm_idx_stat::152.764*1.64] distinct minimizers: 111438932 (43.54% are singletons); average occurrences: 11.631; average spacing: 2.929; total length: 3796066963
[M::worker_pipeline::152.928*1.64] mapped 250 sequences
[M::main] Version: 2.26-r1175
[M::main] CMD: minimap2 -ax splice -I 1000G -t 48 --junc-bed anno.bed genomic.fna test.fq
[M::main] Real time: 153.724 sec; CPU: 251.648 sec; Peak RSS: 25.293 GB
Is this something wrong?
I'm running minimap2 2.26-r1175, but I did not this issue been mentioned in the 2 recent release.
Thank you.
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