The paf output file is empty. Ran this command several times:
minimap2 -I 60G -t 3 --cs -x map-pb --secondary=no --paf-no-hit reference.mmi input.fasta
The log file:
[M::main::75.8630.42] loaded/built the index for 97276 target sequence(s)
[M::mm_mapopt_update::80.7190.45] mid_occ = 1183
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 97276
[M::mm_idx_stat::82.706*0.46] distinct minimizers: 137750817 (21.24% are singletons); average occurrences: 10.516; average spacing: 7.692; total length: 11142783422
The paf output file is empty. Ran this command several times:
minimap2 -I 60G -t 3 --cs -x map-pb --secondary=no --paf-no-hit reference.mmi input.fastaThe log file: [M::main::75.8630.42] loaded/built the index for 97276 target sequence(s) [M::mm_mapopt_update::80.7190.45] mid_occ = 1183 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 97276 [M::mm_idx_stat::82.706*0.46] distinct minimizers: 137750817 (21.24% are singletons); average occurrences: 10.516; average spacing: 7.692; total length: 11142783422
Not sure what happened.