Hi,
I’m trying to download utility mapping databases to be used with the humann_regroup script.
Currently, I’m running humann 3.
But I keep getting the following error when trying to download the mapping dbs.
“Creating subdirectory to install database: /scratch/hasitha/WaterProject/Metagenome/Humann2_files/MappingFiles/utility_mapping
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz”
Below is the command I used:
“[hasitha@pete ~]$ humann_databases --download utility_mapping full /scratch/hasitha/WaterProject/Metagenome/Humann2_files/MappingFiles”
Then I went through this forum and tried using the suggestion to download using wget, but to no avail. Below is the error I got.
[hasitha@pete ~]$ wget “http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz -p /scratch/hasitha
–2021-04-12 23:51:04-- http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
Resolving huttenhower.sph.harvard.edu (huttenhower.sph.harvard.edu)… 140.247.151.38
Connecting to huttenhower.sph.harvard.edu (huttenhower.sph.harvard.edu)|140.247.151.38|:80… connected.
HTTP request sent, awaiting response… 404 Not Found
2021-04-12 23:51:04 ERROR 404: Not Found.”
Would greatly appreciate if someone can mirror the mapping databases to an accessible location and provide the new url.
Thank you very much.
Best Rgds,
Hasitha.
Have you been able to download the files? We had a server outage last week that might’ve affected downloads around this time.
Hi,
I met the same error. When I run the “humann_databases --download uniref uniref90_diamond /home/database/humann3.7_db/”.CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref90_annotated_v201901b_full.tar.gz
This is downloading for me now. It might’ve been another temporary outage?
Hi，
Thanks for your reply. I’ ve download mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar from http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar using wget.
However, I have never been able to successfully run humann3 (v 3.7) and metaphlan (v 4.0), when running to metaphlan. The error message is: Unable to find the mpa_pkl file at: mpa_pklExiting…
I’m guessing that metaphlan may have encountered a problem building the library. I’m going to try to run it again now and was wondering if you have the file or if I have to go through the library build to get it. Perhaps I should just unzip mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar ?
Also, I’ve noticed that I can’t call more threads after running humann, not sure if others have the same problem.
Looking forward to hearing from you and hope all is well!
Hi!
I’m sorry to bother you, but all my problems were solved. I also downloaded these four files at the same URL:mpa_vOct22_CHOCOPhlAnSGB_202212.md5, mpa_vOct22_CHOCOPhlAnSGB_202212.tar, mpa_vOct22_CHOCOPhlAnSGB_202212_marker_ info.txt.bz2, mpa_vOct22_CHOCOPhlAnSGB_202212_species.txt.bz2. unzipped in the database path, it works successfully. I hope my question helps others and I look forward to the release of humann4 .I wish you all the best.
Thanks for the update and glad you were able to solve the issue!
Hi, I am having the error “CRITICAL ERROR: Unable to download and extract from URL: http://huttenhower.sph.harvard.edu/humann_data/full_mapping_v201901b.tar.gz” currently when trying to download the utility mapping. I have tried to use wget, but got “2023-10-17 06:47:02 ERROR 403: Forbidden.” error. Is the server down again? Thanks so much in advance!
Hi @jessieli , Sorry about the downloading errors. We were recently working on migrating our downloads to a new hosting system. Please try again. It should be all set now and hopefully downloads should be a bit faster too!
Thanks!
Lauren
Hi Lauren,
Thank you very much! It is working now and the download was quite fast!
Best,
Jessie
Fantastic! Thanks for the follow up!
Lauren