# Merge\_metaphlan\_tables.py broken

**URL:** https://forum.biobakery.org/t/merge-metaphlan-tables-py-broken/3507
**Category:** MetaPhlAn
**Created:** [April 27, 2022, 6:12pm UTC](https://forum.biobakery.org/t/merge-metaphlan-tables-py-broken/3507 "2022-04-27T18:12:40Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![Chad\_Stachowicz](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/chad_stachowicz/32/1411_2.png) [@Chad\_Stachowicz](https://forum.biobakery.org/u/Chad_Stachowicz)
#### Post date: [April 27, 2022, 6:12pm UTC](https://forum.biobakery.org/t/merge-metaphlan-tables-py-broken/3507/1 "2022-04-27T18:12:40Z")

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After running metaphlan, files with headers are generated however merge\_metaphlan\_tables.py utility always gives the error below:

merge\_metaphlan\_tables found tables without a header including the database version. Exiting.

It appears to be that somehow the merge\_metaphlan\_tables.py script no longer notices the format of the header file.

**Platform (please complete the following information):**  
pip install metaphlan  
3.0.14

file example created from metaphlan:

#mpa\_v30\_CHOCOPhlAn\_201901  
#/Users/chadstachowicz/opt/anaconda3/bin/metaphlan --input\_type fastq /Users/chadstachowicz/Downloads/meta/19APR2016HiSeq\_Run\_Sample\_ATE\_51\_UNCC\_Gibas\_TTAGGCAT\_L006\_R1\_001-sampled.fastq,/Users/chadstachowicz/Downloads/meta/19APR2016HiSeq\_Run\_Sample\_ATE\_51\_UNCC\_Gibas\_TTAGGCAT\_L006\_R2\_001-sampled.fastq --bowtie2out /Users/chadstachowicz/Downloads/meta/ATE\_51.bz2 --nproc 4  
#SampleID Metaphlan\_Analysis  
#clade\_name NCBI\_tax\_id relative\_abundance additional\_species  
k\_\_Bacteria 2 100.0  
k\_\_Bacteria|p\_\_Actinobacteria 2|201174 61.04149  
k\_\_Bacteria|p\_\_Proteobacteria 2|1224 24.83551  
k\_\_Bacteria|p\_\_Firmicutes 2|1239 10.3088

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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: [May 18, 2022, 2:34pm UTC](https://forum.biobakery.org/t/merge-metaphlan-tables-py-broken/3507/2 "2022-05-18T14:34:08Z")

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Hi @Chad_Stachowicz  
Thanks for getting in touch. Have you check whether all the files you are passing to the merge\_metaphlan\_tables are MetaPhlAn output files?