MetaPhlAn database download stalls at 16.57%

Microbial community profiling MetaPhlAn
1

Hello everyone,

I’m running MetaPhlAn for the first time and encountering an issue with the database download. The download starts but consistently stops at 16.57% without any error message. The process then just hangs, and no further progress is made.

I’m using the following command:

metaphlan /mnt/d/leopardWGS/host_removed_alignment_results/02_M1_10K_combined.fastq.gz --input_type fastq --db_dir /mnt/d/humann_databases/chocophlan -x mpa_vJan25_CHOCOPhlAnSGB_202503 --mapout /mnt/d/leopardWGS/humann_output_M1_10K/metaphlan_bowtie2.bz2 --nproc 6 -o /mnt/d/leopardWGS/humann_output_M1_10K/taxonomic_profile.txt

Has anyone experienced this before, or does anyone have an idea what might be causing the download to stop?

Any advice would be greatly appreciated!

metaphlan
/mnt/d/leopardWGS/host_removed_alignment_results/02_M1_10K_combined.fastq.gz
–input_type fastq
–db_dir /mnt/d/humann_databases/chocophlan
-x mpa_vJan25_CHOCOPhlAnSGB_202503
–mapout /mnt/d/leopardWGS/humann_output_M1_10K/metaphlan_bowtie2.bz2
–nproc 6
-o /mnt/d/leopardWGS/humann_output_M1_10K/taxonomic_profile.txt

image
image1106×571 32 KB

2

Hi,

Not sure if this may help, but you could try downloading the database to a folder first using:

metaphlan --install --bowtie2db <path/to/metaphlan_database_folder>

and then including the location to this database in your code:

-x mpa_vJan25_CHOCOPhlAnSGB_202503 --bowtie2db <path/to/metaphlan_database_folder>
1 Like
3

Thank you so much for your suggestion! This solved my problem perfectly. I really appreciate your help.