BBMap not indexing all chromosomes

Question

[elcombe.c]

I'm trying to index a sheep genome. The ./ref/ output only has 7 of the 28 chromosomes there should be. This is what I get (also the same when I run BBMap, I'm using mapPacBio as my reads are nanopore).

chris@chris-Virtual-Machine:~/data$ bbmap/mapPacBio.sh ref=genomic.fna usemodulo=t -Xmx19g -da
java -da -Xmx19g -cp /home/chris/data/bbmap/current/ align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 ref=genomic.fna usemodulo=t -Xmx19g -da
Executing align2.BBMapPacBio [build=1, overwrite=true, minratio=0.40, fastareadlen=6000, ambiguous=best, minscaf=100, startpad=10000, stoppad=10000, midpad=6000, ref=genomic.fna, usemodulo=t, -Xmx19g, -da]
Version 38.84

Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.400
No output file.
Writing reference.
Executing dna.FastaToChromArrays2 [genomic.fna, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=100, midpad=6000, startpad=10000, stoppad=10000, nodisk=false]

Set genScaffoldInfo=true
Writing chunk 1
Writing chunk 2
Writing chunk 3
Writing chunk 4
Writing chunk 5
Writing chunk 6
Writing chunk 7
Set genome to 1

Loaded Reference:       0.185 seconds.
Loading index for chunk 1-7, build 1
No index available; generating from reference genome: /home/chris/data/ref/index/1/chr1-3_index_k12_c2_b1.block
No index available; generating from reference genome: /home/chris/data/ref/index/1/chr4-7_index_k12_c2_b1.block
Indexing threads started for block 0-3
Indexing threads started for block 4-7
Indexing threads finished for block 4-7
Indexing threads finished for block 0-3
Generated Index:        115.925 seconds.
Finished Writing:       2.151 seconds.
No reads to process; quitting.

Total time:             167.243 seconds.

Answer 1

[elcombe.c]

I have now found out that even though they are labelled "chromosome #"...they are not chromosomes, they are "chunks" comprising of multiple chromosomes.

I'm leaving the question up incase anyone else has this confusion.

[GenoMax]

Correct. BBMap uses its own method/format to write the indexes so don't look in the ref and expect to see individual chromosomes.