# Metaphlan4 discordance between relative\_abundance and estimated\_number\_of\_reads

**URL:** <https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086>\
**Category:** MetaPhlAn\
**Created:** [September 19, 2022, 9:19pm UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086 "2022-09-19T21:19:25Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![Hena](https://avatars.discourse-cdn.com/v4/letter/h/85f322/32.png) [@Hena](https://forum.biobakery.org/u/Hena)\
**Post date:** [September 19, 2022, 9:19pm UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086/1 "2022-09-19T21:19:25Z")

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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 - -

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<div class="post-metadata">

**Author:** ![Hena](https://avatars.discourse-cdn.com/v4/letter/h/85f322/32.png) [@Hena](https://forum.biobakery.org/u/Hena)\
**Post date:** [September 23, 2022, 9:15pm UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086/2 "2022-09-23T21:15:34Z")

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

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<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [September 27, 2022, 7:41am UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086/3 "2022-09-27T07:41:02Z")

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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.

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<div class="post-metadata">

**Author:** ![Hena](https://avatars.discourse-cdn.com/v4/letter/h/85f322/32.png) [@Hena](https://forum.biobakery.org/u/Hena)\
**Post date:** [September 28, 2022, 7:29pm UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086/4 "2022-09-28T19:29:04Z")

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Thanks @aitor.blancomiguez !  
Hena

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<div class="post-metadata">

**Author:** ![Hena](https://avatars.discourse-cdn.com/v4/letter/h/85f322/32.png) [@Hena](https://forum.biobakery.org/u/Hena)\
**Post date:** [October 18, 2022, 3:41pm UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086/5 "2022-10-18T15:41:26Z")

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@aitor.blancomiguez just wondering if you had a chance to fix the problem. I am also concerned about the unclassified results. There are 0s in estimated clade values while there are relative abundance values for the same sample. Can you please explain why is that? You can see for the example file that I have placed above UNCLASSIFIED -1 1.80294 - 0 . Just trying to understand how is this possible? I am seeing this in multiple samples.  
Thanks!

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<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [October 18, 2022, 3:48pm UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086/6 "2022-10-18T15:48:38Z")

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Hi @Hena  
We were working in the fix and we are planning to push the new version at the beginning of next week.  
For the Unclassified estimation, we also providing a fix in the next version.

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<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [October 26, 2022, 1:13pm UTC](https://forum.biobakery.org/t/metaphlan4-discordance-between-relative-abundance-and-estimated-number-of-reads/4086/7 "2022-10-26T13:13:14Z")

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Hi @Hena  
The new 4.0.3 version is now available in conda and should solve the issues