kallisto uses one thread instead of 14 assigned for it due to index building from genome building MPHF and creating equivalence classes steps.

[warp-felinidae]

Hello!

kallisto 0.51.0 uses only one thread instead of 14 assigned for it. Is it OK or not? CPU is Intel(R) Xeon(R) CPU E5-2697 v3 @ 2.60GHz, RAM 256 Gb. Fasta file is approximately 6.5 Gb size.

Beginning Now nohup /datastore/01/m_matveeva/kallisto/build/src/kallisto index -i sce_genome.idx -t 14 Secale_cereale.Rye_Lo7_2018_v1p1p1.dna.toplevel.fa

Output: [build] loading fasta file Secale_cereale.Rye_Lo7_2018_v1p1p1.dna.toplevel.fa [build] k-mer length: 31 [build] warning: replaced 155746534 non-ACGUT characters in the input sequence with pseudorandom nucleotides KmerStream::KmerStream(): Start computing k-mer cardinality estimations (1/2) KmerStream::KmerStream(): Start computing k-mer cardinality estimations (1/2) KmerStream::KmerStream(): Finished CompactedDBG::build(): Estimated number of k-mers occurring at least once: 2313881712 CompactedDBG::build(): Estimated number of minimizer occurring at least once: 458715777 CompactedDBG::filter(): Processed 6735226869 k-mers in 8 reads CompactedDBG::filter(): Found 2306160606 unique k-mers CompactedDBG::filter(): Number of blocks in Bloom filter is 15817552 CompactedDBG::construct(): Extract approximate unitigs (1/2) CompactedDBG::construct(): Extract approximate unitigs (2/2) CompactedDBG::construct(): Closed all input files

CompactedDBG::construct(): Splitting unitigs (1/2)

CompactedDBG::construct(): Splitting unitigs (2/2) CompactedDBG::construct(): Before split: 157113240 unitigs CompactedDBG::construct(): After split (1/1): 157113240 unitigs CompactedDBG::construct(): Unitigs split: 0 CompactedDBG::construct(): Unitigs deleted: 0

CompactedDBG::construct(): Joining unitigs CompactedDBG::construct(): After join: 154889278 unitigs CompactedDBG::construct(): Joined 2223962 unitigs [build] building MPHF [build] creating equivalence classes ...

[Yenaled]

Yes, certain steps of building the index cannot be parallelized and thus only use one thread.