Issue
I’m trying to regenerate a SAM file from a previously generated --bowtie2out file in MetaPhlAn.
Command
```
metaphlan A4.bowtie2.bz2
–input_type bowtie2out
–index mpa_vJun23_CHOCOPhlAnSGB_202307
–bowtie2db /metaphlan_analysis/bt2db/
–nproc 8
–samout A4_metaphlan.sam
-o A4_profile_abs.txt
```
Observation
No SAM file is created when I run this command.
Question
Is this expected behaviour when --input_type bowtie2out is used?
Does MetaPhlAn need raw reads as input in order to generate a SAM file with --samout?
Any clarification on whether this is possible without re‑running MetaPhlAn on the raw reads would be appreciated.