i installed metaphlan2.8 with conda in linux.
But i run the code metaphlan2.py SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile.txt
it show this error as follows: Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_latest
Warning: Unable to download https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_latest Traceback (most recent call last):
** File “/home/ftz/anaconda3/bin/metaphlan2.py”, line 1442, in **
** metaphlan2()**
** File “/home/ftz/anaconda3/bin/metaphlan2.py”, line 1164, in metaphlan2**
** pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])**
** File “/home/ftz/anaconda3/bin/metaphlan2.py”, line 570, in check_and_install_database**
** index = resolve_latest_database(bowtie2_db, force_redownload_latest)**
** File “/home/ftz/anaconda3/bin/metaphlan2.py”, line 549, in resolve_latest_database**
** with open(os.path.join(bowtie2_db,‘mpa_latest’)) as mpa_latest:** FileNotFoundError: [Errno 2] No such file or directory: '/home/ftz/anaconda3/bin/metaphlan_databases/mpa_latest’
This url i cannot access,so how to fix it or download this file.
Hi,
we are updating the bioconda package to reflect the changes made in the repository, the database is no more available on bitbucket since we migrated the repository to GitHub.
In the meantime, you can get the latest MetaPhlAn2 from the repository
Thank you reply me!
But i have a new question when i using bioconda .
i am download all realted documents about metaphlan2,so i try it .However,it run with a instruction like “Building Bowtie2 index",and i unzip the ”mpa_v296_CHOCOPhlAn_201901.tar“file and i just get 4 files.It dosen’t have .rev files.
Just like this？
Sorry , I ’m a beginner, so I don’t understand many related things.
and i run the code “metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta -o SRS014476-Supragingival_plaque_profile.txt” again,it shows me another question
and i run the code “metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta -o SRS014476-Supragingival_plaque_profile.txt” again,it shows me another question
It seems that the building process has not finished.
Can you run bowtie2-build mpa_v296_CHOCOPhlAn_201901.fna mpa_v296_CHOCOPhlAn_201901
inside /home/ftz/anaconda3/envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases ?
I used MetaPhlAn version 2.96.1 on 20th of March 2020. I’m rerunning it now using the same installation and get the same error message as the user tongs_fu posted 27 Apr. Is this error message still due to the same issue that you are updating the bioconda package to reflect changes made in the repository?
Warning: Unable to download https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_latest
Traceback (most recent call last):
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan2/bin/metaphlan2.py”, line 1442, in
metaphlan2()
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan2/bin/metaphlan2.py”, line 1164, in metaphlan2
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan2/bin/metaphlan2.py”, line 570, in check_and_install_database
index = resolve_latest_database(bowtie2_db, force_redownload_latest)
File “/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan2/bin/metaphlan2.py”, line 549, in resolve_latest_database
with open(os.path.join(bowtie2_db,‘mpa_latest’)) as mpa_latest:
FileNotFoundError: [Errno 2] No such file or directory: ‘/scratch/project_2001318/metaphlan2/bioconda2_env/metaphlan2/bin/metaphlan_databases/mpa_latest’
hello，i installed metaphlan4.8 with conda in linux on 1st July , 2020. i met the same question with you . how do you deal with the error? Could you share your solution of the error?
Thank you !
Looking forward to your reply
hello，i have not understanded your slution you provided? Could you please instruct me again ? i met the same error. Thanks and looking forward to your reply.
(base) [students@Nebula metaphlan2_analysis]$ metaphlan2.py SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile.txt
Warning: Unable to download https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_latest
Traceback (most recent call last):
File “/public/home/students/miniconda3/bin/metaphlan2.py”, line 1442, in
metaphlan2()
File “/public/home/students/miniconda3/bin/metaphlan2.py”, line 1164, in metaphlan2
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/public/home/students/miniconda3/bin/metaphlan2.py”, line 570, in check_and_install_database
index = resolve_latest_database(bowtie2_db, force_redownload_latest)
File “/public/home/students/miniconda3/bin/metaphlan2.py”, line 549, in resolve_latest_database
with open(os.path.join(bowtie2_db,‘mpa_latest’)) as mpa_latest:
FileNotFoundError: [Errno 2] No such file or directory: ‘/public/home/students/miniconda3/bin/metaphlan_databases/mpa_latest’
Hi, you are installing an older MetaPhlAn build. In order to use the most recent and working one, you should configure first the conda installation, if it was not already done:
then,
create a new one with python 3.7: conda create -n metaphlan-3.0 python=3.7
install MetaPhlAn 3 in the new environment: conda activate metaphlan-3.0 && conda install -c bioconda metaphlan
Thanks for your reply . I performed commands you instructed. But I have a new question , i do not find the tutorial of Metaphlan3 . I am a newbie . I have using the tutorial of Metaphlan2 , but it reported an error . Thanks ! Looking forward your reply.
(metaphlan-3.0) [students@Nebula metaphlan2_analysis]$ metaphlan3.py SRS014459-Stool.fasta.gz --input_type fasta --nproc 4 > SRS014459-Stool_profile.txt
-bash: metaphlan3.py: command not found
