Metaphlan4 discordance between relative_abundance and estimated_number_of_reads

I am using metaphlan4 in a conda environment. When I look at the profile results, there are nonzero relative_abundance value while the estimated_number_of_reads_from_the_clade is 0 or -. Can you please explain how is this possible? I might have missed something. You can look at the unclassified clade_name or t__SGB7962 for example. There are a few others here with that issue.

The profile output for one of my samples is:
#mpa_vJan21_CHOCOPhlAnSGB_202103
#/bulk/IMCbinf_bulk/hramay/projects/Arrieta/PC1000/antibiotic_babies/analysis/metaphlan4/.snakemake/conda/87013b619fc67c1a9da33c332c64e376/bin/metaphlan -t rel_ab_w_read_stats --unclassified_estimation output_merged_sam/merged_data/S00CI-0093_S54.fastq --add_viruses --input_type fastq --bowtie2db /bulk/IMCshared_bulk/shared/dbs/metaphlan4 --bowtie2out output_merged_sam/metaphlan/S00CI-0093_S54_bowtie2.bz2 --nproc 8 -o output_merged_sam/metaphlan/S00CI-0093_S54_profile.txt
#SampleID Metaphlan_Analysis
#estimated_reads_mapped_to_known_clades:428080
#clade_name clade_taxid relative_abundance coverage estimated_number_of_reads_from_the_clade
UNCLASSIFIED -1 1.80294 - 0
k__Bacteria 2 98.19706 0.01638 428080
k__Bacteria|p__Firmicutes 2|1239 74.6264 0.01244 269612
k__Bacteria|p__Actinobacteria 2|201174 11.07805 0.00185 31318
k__Bacteria|p__Proteobacteria 2|1224 6.34208 0.00106 37898
k__Bacteria|p__Bacteroidetes 2|976 6.15053 0.00103 35742
k__Bacteria|p__Firmicutes|c__Bacilli 2|1239|91061 61.71549 0.01029 186348
k__Bacteria|p__Firmicutes|c__Clostridia 2|1239|186801 12.91091 0.00215 44748
k__Bacteria|p__Actinobacteria|c__Actinobacteria 2|201174|1760 11.07805 0.00185 26844
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 2|1224|1236 6.34208 0.00106 32484
k__Bacteria|p__Bacteroidetes|c__Bacteroidia 2|976|200643 6.15053 0.00103 30636
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales 2|1239|91061|186826 61.71549 0.01029 155290
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales 2|1239|186801|186802 12.91091 0.00215 37290
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales 2|201174|1760|85004 11.07805 0.00185 22370
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 2|976|200643|171549 6.15053 0.00103 25530
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales 2|1224|1236|91347 6.13684 0.00102 25930
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales 2|1224|1236|72274 0.20524 3e-05 1140
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae 2|1239|91061|186826|81852 61.71549 0.01029 124232
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae 2|1239|186801|186802|186803 12.91091 0.00215 29832
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae 2|201174|1760|85004|31953 11.07805 0.00185 17896
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae 2|1224|1236|91347|543 6.13684 0.00102 20744
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae 2|976|200643|171549|815 5.0969 0.00085 16532
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified 2|976|200643|171549| 1.05363 0.00018 3892
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae 2|1224|1236|72274|135621 0.20524 3e-05 912
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus 2|1239|91061|186826|81852|1350 61.71549 0.01029 93174
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Mediterraneibacter 2|1239|186801|186802|186803|2316020 12.91091 0.00215 22374
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium 2|201174|1760|85004|31953|1678 11.07805 0.00185 13422
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia 2|1224|1236|91347|543|561 6.13684 0.00102 15558
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 2|976|200643|171549|815|816 5.0969 0.00085 12399
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Phocaeicola 2|976|200643|171549||909656 1.05363 0.00018 2919
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas 2|1224|1236|72274|135621|286 0.20524 3e-05 684
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus_faecalis 2|1239|91061|186826|81852|1350|1351 61.71549 0.01029 62116
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Mediterraneibacter|s__Ruminococcus_gnavus 2|1239|186801|186802|186803|2316020|33038 12.91091 0.00215 14916
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_longum 2|201174|1760|85004|31953|1678|216816 11.07805 0.00185 8948
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 2|1224|1236|91347|543|561|562 6.13684 0.00102 10372
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_uniformis 2|976|200643|171549|815|816|820 5.0969 0.00085 8266
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Phocaeicola|s__Phocaeicola_dorei 2|976|200643|171549||909656|357276 1.05363 0.00018 1946
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa 2|1224|1236|72274|135621|286|287 0.20524 3e-05 456
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus_faecalis|t__SGB7962 2|1239|91061|186826|81852|1350|1351| 61.71549 - -
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Mediterraneibacter|s__Ruminococcus_gnavus|t__SGB4584 2|1239|186801|186802|186803|2316020|33038| 12.91091 - -
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_longum|t__SGB17248 2|201174|1760|85004|31953|1678|216816| 11.07805 - -
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__SGB10068 2|1224|1236|91347|543|561|562| 6.13684 - -
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_uniformis|t__SGB1836_group 2|976|200643|171549|815|816|820| 5.0969 - -
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Phocaeicola|s__Phocaeicola_dorei|t__SGB1815 2|976|200643|171549||909656|357276| 1.05363 - -
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa|t__SGB12320 2|1224|1236|72274|135621|286|287| 0.20524 - -

Hi,
Does anyone has input on this issue?
Thanks!
Hena

Hi @Hena
sorry for the late reply. It seems that the “-t rel_ab_w_read_stats” is not working at the SGB (t__) level of the profiles. Thanking for reporting this issue, I will start working on a fix asap and will let you know when it is out there.

Thanks @aitor.blancomiguez !
Hena