MetaPhlan Database

Microbial community profiling HUMAnN
1

HUMANn 3.6.1
I had downloaded the database using command “http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz”. If I run the following command-
humann --input examples/demo.fastq.gz --output demo_humann --threads 16
Error-
Running metaphlan …

CRITICAL ERROR: Error executing: /home/gmpl/miniconda3/envs/functional_meta/bin/metaphlan /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/demo_humann/demo_humann_temp/tmp4gblt7o6/tmpj27r9pas -t rel_ab -o /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/demo_humann/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/demo_humann/demo_humann_temp/demo_metaphlan_bowtie2.txt --nproc 16

Error message returned from metaphlan :

Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

\Downloading and uncompressing indexes

File /home/gmpl/miniconda3/envs/functional_meta/lib/python3.11/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar already present!

File /home/gmpl/miniconda3/envs/functional_meta/lib/python3.11/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5 already present!
MD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded
Can you please suggest what to do to run this command?

2

sorry, the command was wget -c http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz

3

Can you please help as I am not able to solve this issue?

4

Hello, If you remove the partial download files and re-run it should solve the error. The files appear to be at /home/gmpl/miniconda3/envs/functional_meta/lib/python3.11/site-packages/metaphlan/metaphlan_databases/ on your system. Sorry for any confusion and I hope the next download goes well!

Thanks!
Lauren

5

humann --input NanoFilt_b1_hc75_l200_q8.fastq.gz --output bg1234_b1_humann --nucleotide-database /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/chocophlan/chocophlan/ --threads 12 --protein-database /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/uniref/uniref90_annotated_v201901b_full

I am using this above command and getting following error again
CRITICAL ERROR: Error executing: /home/gmpl/miniconda3/envs/functional_meta/bin/metaphlan /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/bg1234_b1_humann/NanoFilt_b1_hc75_l200_q8_humann_temp/tmpvfod5o4s/tmp8wengwfe -t rel_ab -o /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/bg1234_b1_humann/NanoFilt_b1_hc75_l200_q8_humann_temp/NanoFilt_b1_hc75_l200_q8_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/bg1234_b1_humann/NanoFilt_b1_hc75_l200_q8_humann_temp/NanoFilt_b1_hc75_l200_q8_metaphlan_bowtie2.txt --nproc 12

Error message returned from metaphlan :

Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

\Downloading and uncompressing indexes

File /home/gmpl/miniconda3/envs/functional_meta/lib/python3.11/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar already present!

File /home/gmpl/miniconda3/envs/functional_meta/lib/python3.11/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5 already present!
MD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded

**I had downloaded the chocophlan databases today in one go **
Please help for this issue.

6

humann --input NanoFilt_b1_hc75_l200_q8.fastq.gz --output bg1234_b1_humann --nucleotide-database /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/chocophlan/chocophlan/ --threads 12 --protein-database /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/uniref/uniref90_annotated_v201901b_full

I am using above command after your suggestion to remove the partial downloaded files and again below error I am getting
Output files will be written to: /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/bg1234_b1_humann
Decompressing gzipped file …

Removing spaces from identifiers in input file …

Running metaphlan …

CRITICAL ERROR: Error executing: /home/gmpl/miniconda3/envs/functional_meta/bin/metaphlan /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/bg1234_b1_humann/NanoFilt_b1_hc75_l200_q8_humann_temp/tmp5rf8du0k/tmp6xlbx8of -t rel_ab -o /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/bg1234_b1_humann/NanoFilt_b1_hc75_l200_q8_humann_temp/NanoFilt_b1_hc75_l200_q8_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /media/gmpl/Data_Raw/bscmonsoon/humann-3.6.1/bg1234_b1_humann/NanoFilt_b1_hc75_l200_q8_humann_temp/NanoFilt_b1_hc75_l200_q8_metaphlan_bowtie2.txt --nproc 12

Error message returned from metaphlan :

Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

\Downloading and uncompressing indexes

File /home/gmpl/miniconda3/envs/functional_meta/lib/python3.11/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar already present!

Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5
Downloading file of size: 0.00 MB
MD5 checksums do not correspond! If this happens again, you should remove the database files and rerun MetaPhlAn so they are re-downloaded

7

Thank you for the additional information. Can you remove this original partial database file and try running again?

/home/gmpl/miniconda3/envs/functional_meta/lib/python3.11/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar

I think removing the file should resolve the error you are seeing.

Thank you,
Lauren

8

Hi, I got the same error as @self_shubham.

Error message returned from metaphlan :

Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

\Downloading and uncompressing indexes

Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar
Downloading file of size: 20348.27 MB
1123.78 MB 5.52 % 0.07 MB/sec 4341 min 28 sec
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.tar

Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5

Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5
File “/home/priscilla/anaconda3/envs/humann3/lib/python3.10/site-packages/metaphlan/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_bt2.md5” not found!
MD5 checksums not found, something went wrong!

I wonder if something is missing with the .md5 file. Hope to get a solution from this as I have been trying to remove the metaphlan database file and re-run the command again but it doesn’t works.

9

Hi Priscilla, I just got the same exact error message when trying to install the database with metaphlan --install. Were you able to resolve the issue?

Thank you,
Anna

1 Like
10

have you resolved the issue?
Thank you,
yc_lu