# Metaphlan4 estimated\_number\_of\_reads

**URL:** <https://forum.biobakery.org/t/metaphlan4-estimated-number-of-reads/6247>\
**Category:** MetaPhlAn\
**Created:** [November 24, 2023, 9:30am UTC](https://forum.biobakery.org/t/metaphlan4-estimated-number-of-reads/6247 "2023-11-24T09:30:50Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Junyan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/junyan/32/2551_2.png) [@Junyan](https://forum.biobakery.org/u/Junyan)\
**Post date:** [November 24, 2023, 9:30am UTC](https://forum.biobakery.org/t/metaphlan4-estimated-number-of-reads/6247/1 "2023-11-24T09:30:50Z")

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I found there is a discrepancy in estimated\_number\_of\_reads between inputting two separate fastq files and inputting a single concatenated fastq file for paired-end data when using Metaphlan4.  
I used `cat` command to concatenate paired-end reads.

Output for two separate fastq input:  
the profile output for input of two separate fastq:  
#mpa\_vOct22\_CHOCOPhlAnSGB\_202212  
#/software/MetaPhlAn/4.0.6/bin/metaphlan ./Clean/SRR14092160\_1\_Clean.fastq.gz,./Clean/SRR14092160\_2\_Clean.fastq.gz --input\_type fastq --index mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --bowtie2db /resources/fdb/Software\_bundle/MetaPhlAn4/database/mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --bowtie2out ./metaphlan4/SRR14092160.bowtie2.bz2 --nproc 12 -t rel\_ab\_w\_read\_stats --unclassified\_estimation  
#71940062 reads processed   
#SampleID Metaphlan\_Analysis   
#estimated\_reads\_mapped\_to\_known\_clades:59117153  
#clade\_name clade\_taxid relative\_abundance coverage estimated\_number\_of\_reads\_from\_the\_clade  
UNCLASSIFIED -1 17.1838 - _ **12822909** _  
k\_\_Bacteria 2 82.81279 20.98874 _ **59106513** _  
k\_\_Eukaryota 2759 0.00341 0.00086 _ **10640** _

the profile output for input of single fastq:  
#mpa\_vOct22\_CHOCOPhlAnSGB\_202212  
#/software/MetaPhlAn/4.0.6/bin/metaphlan ./Clean/SRR14092160\_merge\_Clean.fastq --input\_type fastq --index mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --bowtie2db /resources/fdb/Software\_bundle/MetaPhlAn4/database/mpa\_vOct22\_CHOCOPhlAnSGB\_202212 --bowtie2out ./metaphlan4/SRR14092160.bowtie2.bz2 --nproc 12 -t rel\_ab\_w\_read\_stats --unclassified\_estimation  
#71940062 reads processed   
#SampleID Metaphlan\_Analysis   
#estimated\_reads\_mapped\_to\_known\_clades:59117218  
#clade\_name clade\_taxid relative\_abundance coverage estimated\_number\_of\_reads\_from\_the\_clade  
UNCLASSIFIED -1 17.18374 - _ **12822844** _  
k\_\_Bacteria 2 82.81284 20.98876 _ **59106578** _  
k\_\_Eukaryota 2759 0.00341 0.00086 _ **10640** _

What causes the discrepancy ?

Thanks a lot!

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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:** [March 5, 2024, 11:36am UTC](https://forum.biobakery.org/t/metaphlan4-estimated-number-of-reads/6247/2 "2024-03-05T11:36:14Z")

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This is interesting, could you trace back the inconsistencies to the t\_\_SGB level?