[PinkTips]

When using non-quality-trimmed fastq for BBSplit, it worked just fine!

My quality-trimming step uses BBDuk -- this command:

./bbmap/bbduk.sh in=nonrRNA_bran11.fastq out=QualTrimmed_bran11.fastq qtrim=r trimq=10 overwrite=true

Thoughts on how I should revise this to prevent an invalid file format error when moving to BBSplit?

I really appreciate your helpful (and quick!) replies!

[GenoMax]

That command looks fine. Perhaps you had a one time corruption with the file you got.

[PinkTips]

Thank you for your help!

I have just one more question regarding the output from BBSplit.

-------------- Results ---------------

Genome: 1
Key Length: 13
Max Indel: 20
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 1829806 (416340827 bases)

Mapping: 1630.950 seconds.
Reads/sec: 1121.93
kBases/sec: 255.28


Read 1 data: pct reads num reads pct bases num bases

mapped: 13.1904% 241358 13.0507% 54335231
unambiguous: 9.5835% 175359 9.5952% 39948829
ambiguous: 3.6069% 65999 3.4554% 14386402
low-Q discards: 0.0000% 0 0.0000% 0

perfect best site: 1.9436% 35564 1.8453% 7682929
semiperfect site: 1.9468% 35623 1.8485% 7695929

Match Rate: NA NA 96.0824% 52522434
Error Rate: 75.3143% 204784 3.8796% 2120757
Sub Rate: 73.8546% 200815 2.3134% 1264595
Del Rate: 14.3653% 39060 0.6014% 328726
Ins Rate: 16.4704% 44784 0.9649% 527436
N Rate: 3.9234% 10668 0.0380% 20766

Total time: 1715.910 seconds.

Since I had three reference sequences, is the "Genome: 1" referring to the combined reference of all three that I listed under the "ref=" parameter?

ref=p.americana_genome.fasta,Blattabacterium_genome.fasta,Blattabacterium_plasmid.fasta