search

DiltheyLab / MetaMaps

Long-read metagenomic analysis
Other
96 stars 23 forks source link

Mapping step spent very long time is normal? #53

Closed J-I-P closed 12 months ago

J-I-P commented 3 years ago

Hi, everyone I used MetaMaps to mapping, and it spent a large time. My dataset is below: reference: databases/miniSeq+H/DB.fa query: two_reads.fasta image maxmemory: 50 threads: 20 image image My Query is only two reads, but mapping time needs ten hours. Is it correct and normal?

Thanks for any advice on this!

J-I-P commented 3 years ago

Here is my command: ./metamaps mapDirectly --all -r databases/miniSeq+H/DB.fa -q sample_0.001_single.fastq -o 0.001_single_DB_m50_t20 --maxmemory 50 -t 20

AlexanderDilthey commented 12 months ago

Hey @J-I-P,

Indexing the database can take a substantial amount of time - when you process a file with more reads, runtime should go up sub-linearly.

Best wishes

Alex