hisat2-build

Question

[Bjorn]

Hello,

I am running this command on my reference genome found https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003957565.2/

hisat2-build -p 16 /Volumes/cachannel/ZebraFinchBrain/GCF_003957565.2/ncbi_dataset/data/GCF_003957565.2/GCF_003957565.2_bTaeGut1.4.pri_genomic.fna /Volumes/cachannel/ZebraFinchBrain/reftwo/referencegenome2

However I get this error where no A nucleotides are counted. This is odd because in the .fna file it is clear that they are present.

Returning block of 12034714 for bucket 115
Exited GFM loop
fchr[A]: 0
fchr[C]: 306050462
fchr[G]: 526435244
fchr[T]: 746725372
fchr[$]: 1052636474
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 355107337 bytes to primary GFM file: /Volumes/cachannel/ZebraFinchBrain/reftwo/referencegenome2.1.ht2
Wrote 263159124 bytes to secondary GFM file: /Volumes/cachannel/ZebraFinchBrain/reftwo/referencegenome2.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 462917771 bytes to primary GFM file: /Volumes/cachannel/ZebraFinchBrain/reftwo/referencegenome2.5.ht2
Wrote 267955020 bytes to secondary GFM file: /Volumes/cachannel/ZebraFinchBrain/reftwo/referencegenome2.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
    len: 1052636474
    gbwtLen: 1052636475
    nodes: 1052636475
    sz: 263159119
    gbwtSz: 263159119
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 65789780
    offsSz: 263159120
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 5482482
    numLines: 5482482
    gbwtTotLen: 350878848
    gbwtTotSz: 350878848
    reverse: 0
    linearFM: Yes

[GenoMax]

That is a bit odd. Even though it is showing 0 for A have you checked to see if the index works. Perhaps that is a bug of some sort.

[Bjorn]

Yeah, It doesn't work. I get this error

Error: Encountered internal HISAT2 exception (#1)