Hi,

I'm using BBNorm to separate my reads by kmer depth, and I encountered what seemed to me to be strange behaviour. When I adjust the bin depths, I am getting inconsistent binning of reads, at least as far as I understand the aim of the program.

For instance, if I set a high bin depth at 200 and a low bin depth at 10, I will get a different number of reads in the high depth bin compared to when I set it at 200 and 100. Is that expected? My understanding is that the high depth reads (>200) should all be put in the highdepth output, so why would a different low depth setting change how many were high depth?

This leads to problems where I will get more reads using a 250 high depth bin than a 200 high depth bin because the low depth is different. I'll include the commands I ran to test this when I noticed that.

bbnorm.sh in1=trim_dedup_Anacalosa_R1.fastq.gz in2=trim_dedup_Anacalosa_R2.fastq.gz outhigh=high250_td_Anacalosa.fastq.gz outlow=low100_td_Anacalosa.fastq.gz outmid=mid_td_Anacalosa.fastq.gz passes=1 highbindepth=250 lowbindepth=100

Total reads in:         74158538    74.090% Kept
Low bin reads:          48960818    66.022%
Mid bin reads:          7333512     9.889%
High bin reads:         17864208    24.089%

bbnorm.sh in1=trim_dedup_Anacalosa_R1.fastq.gz in2=trim_dedup_Anacalosa_R2.fastq.gz outhigh=test1high.fastq.gz outlow=test1low.fastq.gz outmid=test1mid.fastq.gz passes=1 highbindepth=200 lowbindepth=100

Total reads in:         74158538    74.081% Kept
Low bin reads:          48959146    66.020%
Mid bin reads:          5925252     7.990%
High bin reads:         19274140    25.990%


 bbnorm.sh in1=trim_dedup_Anacalosa_R1.fastq.gz in2=trim_dedup_Anacalosa_R2.fastq.gz outhigh=test2high.fastq.gz outlow=test2low.fastq.gz outmid=test2mid.fastq.gz passes=1 highbindepth=200 lowbindepth=10

Total reads in:         74158538    74.076% Kept
Low bin reads:          21759858    29.342%
Mid bin reads:          36943402    49.817%
High bin reads:         15455278    20.841%

 bbnorm.sh in1=trim_dedup_Anacalosa_R1.fastq.gz in2=trim_dedup_Anacalosa_R2.fastq.gz outhigh=test3high.fastq.gz outlow=test3low.fastq.gz outmid=test3mid.fastq.gz passes=1 highbindepth=250 lowbindepth=10

Total reads in:         74158538    74.092% Kept
Low bin reads:          21728446    29.300%
Mid bin reads:          38034948    51.289%
High bin reads:         14395144    19.411%

Any idea why it is behaving this way or what I'm misunderstanding?