# The number of "samples" in strainphlan's result file exceeded the number of my macro gene sequencing samples

**URL:** https://forum.biobakery.org/t/the-number-of-samples-in-strainphlans-result-file-exceeded-the-number-of-my-macro-gene-sequencing-samples/7027
**Category:** StrainPhlAn
**Created:** [May 10, 2024, 11:31am UTC](https://forum.biobakery.org/t/the-number-of-samples-in-strainphlans-result-file-exceeded-the-number-of-my-macro-gene-sequencing-samples/7027 "2024-05-10T11:31:44Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![LuXX](https://avatars.discourse-cdn.com/v4/letter/l/e19b73/32.png) [@LuXX](https://forum.biobakery.org/u/LuXX)
#### Post date: [May 10, 2024, 11:31am UTC](https://forum.biobakery.org/t/the-number-of-samples-in-strainphlans-result-file-exceeded-the-number-of-my-macro-gene-sequencing-samples/7027/1 "2024-05-10T11:31:44Z")

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strainphlan -s \*json.bz2 --print\_clades\_only -o ./strainphlan\_result --nproc 10 --marker\_in\_n\_samples\_perc 20 \> clades.txt

Fri May 10 16:59:17 2024: Start StrainPhlAn 4.1.0 execution  
Fri May 10 16:59:17 2024: Loading MetaPhlAn mpa\_vJun23\_CHOCOPhlAnSGB\_202307 database…  
Fri May 10 16:59:45 2024: Done.  
Fri May 10 16:59:57 2024: Processing samples…  
Fri May 10 17:00:01 2024: Constructing the big marker matrix  
Fri May 10 17:00:02 2024: Checking 742 species  
Fri May 10 17:00:03 2024: Done.  
Fri May 10 17:00:04 2024: Detected clades:  
Fri May 10 17:00:04 2024: t\_\_SGB17237: in 173 samples.  
Fri May 10 17:00:04 2024: t\_\_SGB17248: in 95 samples.  
Fri May 10 17:00:04 2024: t\_\_SGB8007\_group: in 8 samples.  
Fri May 10 17:00:04 2024: t\_\_SGB14483: in 5 samples.  
Fri May 10 17:00:04 2024: Done.  
Fri May 10 17:00:04 2024: Finish StrainPhlAn 4.1.0 execution (47.41 seconds): Results are stored at “./02\_strainphlan\_result”

I only took 30 metaphlan results as input, and I wondered what “sample” refers to in the appeal text.  
And there should be more than 4 common SGB in all my samples.

I then took the next step and executed the command.  
strainphlan -s 02\_strainphlan\_result/\*.json.bz2 -m CladeMarkers/t\_\_SGB14483.fna -o Output/t\_\_SGB14483 -c t\_\_SGB14483 -d ./mpa\_vJun23\_CHOCOPhlAnSGB\_202307.pkl --nproc 10 --mutation\_rates --phylophlan\_mode fast  
next error  
[Error] The main inputs samples + references are less than 4Fri May 10 17:52:21 2024: Stop StrainPhlAn execution.

The result is unacceptable to me. I’m just looking for a shared strain in my matching mother and baby samples.

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### Author: ![Michal\_Puncochar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/michal_puncochar/32/2321_2.png) [@Michal\_Puncochar](https://forum.biobakery.org/u/Michal_Puncochar)
#### Post date: [June 4, 2024, 11:33am UTC](https://forum.biobakery.org/t/the-number-of-samples-in-strainphlans-result-file-exceeded-the-number-of-my-macro-gene-sequencing-samples/7027/2 "2024-06-04T11:33:09Z")

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Hello @LuXX ,

unfortunately there was an error in the implementation of the` --print_clades_only` mode which we fixed in the 4.1.1 version ([Release 4.1.1 · biobakery/MetaPhlAn · GitHub](https://github.com/biobakery/MetaPhlAn/releases/tag/4.1.1)).

Then for the second error please check how many files are fitting the `02_strainphlan_result/*.json.bz2` pattern. In the first command you’re using `*json.bz2` without the folder so I’m not sure how is your file structure set up.