# StrainPhlAn no clades found

**URL:** https://forum.biobakery.org/t/strainphlan-no-clades-found/6017
**Category:** StrainPhlAn
**Created:** [October 8, 2023, 3:32pm UTC](https://forum.biobakery.org/t/strainphlan-no-clades-found/6017 "2023-10-08T15:32:55Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![amiyaal](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/amiyaal/32/2463_2.png) [@amiyaal](https://forum.biobakery.org/u/amiyaal)
#### Post date: [October 8, 2023, 3:32pm UTC](https://forum.biobakery.org/t/strainphlan-no-clades-found/6017/1 "2023-10-08T15:32:55Z")

</div>

Hello,

I am using StrainPhlAn for the 1st time. When running it with --print\_clades\_only to find suitable clades (on 18 samples, but I’ve got more) I get an empty print\_clades\_only.tsv file with no clades. I’d be thankful for an explanation of what I’m doing wrong.

```plaintext
mkdir -p sams
mkdir -p bowtie2
mkdir -p profiles
for f in fastq/Ilany*
  do
echo "Running MetaPhlAn on ${f}"
bn=$(basename ${f})
metaphlan ${f} --input_type fastq -s sams/${bn}.sam.bz2 --bowtie2out bowtie2/${bn}.bowtie2.bz2 -o profiles/${bn}_profiled.tsv --bowtie2db ~/Documents --nproc 8
done

mkdir -p consensus_markers
sample2markers.py -i sams/*.sam.bz2 -o consensus_markers -n 8 -d ~/Documents/mpa_vOct22_CHOCOPhlAnSGB_202212.pkl

strainphlan -s consensus_markers/*.pkl -o output --print_clades_only -d ~/Documents/mpa_vOct22_CHOCOPhlAnSGB_202212.pkl

```