Scientific notation in abundance file result in rounding errors

[donovan-h-parks]

Hi. We've run into a small issue that we are hoping can be fixed in the next release. The abundance profile produced with the -abundances flag reports pair counts in scientific notation when numbers get large, e.g.:

# query summary: number of queries mapped per taxon
# rank  name    taxid   number of reads     abundance
domain  Archaea     439684927   461     0.0130496%
domain  Bacteria    609216830   1.05068e+06     29.7417%

This can result in small errors due to rounding. For example, in this case there is really 1050675 Bacterial read pairs, but it gets rounded up to 1050680. While having 5 extra read pairs is minor in terms of the resulting abundance estimates it makes it challenging to track the fait of all reads. In our code, we have a check that the number of input reads is equal to the number of reads in the MetaCache abundance profile (including unclassified). This is just a unit test to ensure our parsing is correct and that no reads are lost during any manipulation of data, but, more generally, not being able to account for all reads is a bit scary.

I imagine the intent is for this profile to produced integers, so am hoping this can be fixed in the next release. Thanks.

[muellan]

This is clearly a bug. I'll look into it.

[donovan-h-parks]

Thanks André. Much appreciated.

[muellan]

The latest release should fix this issue.

[muellan]

@donovan-h-parks: could you maybe check, if this fixes your outputs?

[donovan-h-parks]

Hi @muellan,

I'm still encountering this issue in v2.4.2, e.g.:

# query summary: number of queries mapped per taxon
# rank  name    taxid   number of reads     abundance
domain  Bacteria    81602897    9.96505e+06     13.2788%
domain  Archaea     1337977286  13005   0.0173297%
phylum  Cyanobacteriota     15887558    3226    0.00429877%
phylum  Fibrobacterota  31572563    34  4.53063e-05%
phylum  Spirochaetota   39784000    1217    0.0016217%
...

I run MetaCache as follows:

> metacache query my_db P00001898_1.fq.gz P0000189_2.fq.gz -pairfiles -no-map -taxids -lineage -separate-cols -separator      -threads 32 -abundances metacache_raw_profile.tsv -lowest subspecies -out metacache_read_classification.log

MetaCache version details:

> metacache info
------------------------------------------------
MetaCache version    2.4.2 (20240311)
database version     20200820
------------------------------------------------
...