Hi all
I am fir the first time installing biobakery, during installation I am getting error in running the code:
biobakery_workflows_database:
tried my ways but failed.followed some tutorials and guides also
kindly help and mention the command I will be running in my case
like you did it here
Problem 1
biobakery_workflows_databases --install wmgx
Installing humann utility mapping database
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
Downloading file of size: 2.55 GB
2.55 GB 100.00 % 1.49 MB/sec 0 min -0 sec
Extracting: /home/qiime2/biobakery_workflows_databases/humann/full_mapping_v201901.tar.gz
Database installed: /home/qiime2/biobakery_workflows_databases/humann/utility_mapping
HUMAnN configuration file updated: database_folders : utility_mapping = /home/qiime2/biobakery_workflows_databases/humann/utility_mapping
Generating strainphlan fasta database
Could not locate a Bowtie index corresponding to basename “/home/qiime2/miniconda/envs/kneaddata/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901”
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/qiime2/miniconda/envs/abmiguez kneaddata/bin/bowtie2-inspect-s --wrapper basic-0 /home/qiime2/miniconda/envs/kneaddata/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901
Unable to install database. Error running command: bowtie2-inspect /home/qiime2/miniconda/envs/kneaddata/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 > /home/qiime2/biobakery_workflows_databases/strainphlan_db_markers/all_markers.fasta
Problem 2
And secondly If hopefully I am done with installation, please let me know the tutorial I will following for analysis my shotgun datsets
Hi all
any one here who can help out
Thanks
Hello, Thank you for the detailed post and sorry for the slow response. If you update your workflows installation to the latest version, it should resolve the error. Alternatively you can install the MetaPhlAn v30 database to resolve the error. There is a tutorial for the bioBakery workflows that will walk you through running the workflows on shotgun data. biobakery_workflows · biobakery/biobakery Wiki · GitHub
Thank you,
Lauren
Hi @lauren.j.mciver
Thank you for your help
But the issue still exists.
Can you please be a bit more elaborative on installation process.
Thanks and regards.
Sure! If you used conda for the install you can run “conda upgrade” to update to the latest version.
Thank you,
Lauren
Hi @lauren.j.mciver
Sorry again I tried to install again
and failed gave the error.
please finds the detailed error below
conda install -c biobakery workflows
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
** - workflows**
Current channels:
** - Linux 64 :: Anaconda.org**
** - Noarch :: Anaconda.org**
** - main/linux-64**
** - main/noarch**
** - r/linux-64**
** - r/noarch**
To search for alternate channels that may provide the conda package you’re
looking for, navigate to
** https://anaconda.org**
and use the search bar at the top of the page.
Kindly suggest the steps, I need to follow for proper installation
thanks and regards
Hi @mallamuneer , If you try it again with “conda install -c biobakery biobakery_workflows” I think it should resolve the error. Let me know how it goes.
Thanks!
Lauren
Hi @lauren.j.mciver
Sorry
I think I have mentioned wrong command. I forget to put (_) between biobakery and workflows.
Is it so
Thanks and regardd
Hi @lauren.j.mciver
there is some serious compatibility issues with the two systems that i am using
Again, this command conda install -c biobakery biobakery_workflows ran in my laptop, but later on gave error because of citing memory error
In case of my desktop while running the same command it gave this error
qiime2@qiime2core2020-11:~$ conda install -c biobakery biobakery_workflows
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
**Solving environment: | **
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
**failed **
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
** - biobakery_workflows → python[version=‘>=2.7,<2.8.0a0|>=3.7,<3.8.0a0’]**
Your python: python=3.8
If python is on the left-most side of the chain, that’s the version you’ve asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
** - feature:/linux-64::__glibc==2.27=0**
** - python=3.8 → libgcc-ng[version=‘>=11.2.0’] → __glibc[version=‘>=2.17’]**
Your installed version is: 2.27
kindly suggest how to solve this error
thanks
Hi @lauren.j.mciver
Any leads to get out of this trouble.
Kindly suggest
Thanks and regards
Hi @lauren.j.mciver
i managed to Install the workflow by using pip install
but while downloading the Chocophlan almost after 50% downloading, it gives error showing can not decode the checksum number
kindly please help
Hi @mallamuneer , I am glad to hear you were able to download the software. Have you tried downloading the database a couple times? High loads on the server cause the download speed to slow down.
Thank you,
Lauren
Hi@ lauren.j.mciver
Thank you,
Yes I trued multiple times but It says can’t decode the check sum.
Any alternative way to install manually,
If so please mention the commands to install
Secondly I hope I will get it installed,
Then I need a simple guidance to run the command (i have paired end data).
Thanks and regards
The url should be included in the error message. It will depend on the database version you are trying to install. You can download the database manually (if pre-build, if not build it with bowtie2) and then place it in the expected folder or a folder that you select.
The basic command would be “$ biobakery_workflows wmgx --input <INPUT_FOLDER> --output <OUTPUT_FOLDER>” . So hopefully once it is all installed it should be easy to get up and running!
Thanks!
Lauren
Thank you again
Can you please mention how to build the database with bowtie2
As I don’t know it.
Thanks and Reagrds
Hi @ lauren.j.mciver
Thank you again
Please check the error
I am again facing
metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db bowtie2
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_vJan21_CHOCOPhlAnSGB_202103_bt2.tar
Downloading file of size: 19909.64 MB
14714.07 MB 73.90 % 1.81 MB/sec 47 min 45 sec
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan21_CHOCOPhlAnSGB_202103_bt2.tar
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan21_CHOCOPhlAnSGB_202103_bt2.md5
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan21_CHOCOPhlAnSGB_202103_bt2.md5
File “bowtie2/mpa_vJan21_CHOCOPhlAnSGB_202103_bt2.md5” not found!
MD5 checksums not found, something went wrong!
Please help out
Hi @lauren.j.mciver
I trust you are well
After getting the above mentioned error, I downloaded the database manually.
Please guide me here how to move forward ( I mean how to build it with bowtie2), any code or command needed please mention.
thanks and regards
Hi @mallamuneer , If you downloaded the files from the URL Index of /biobakery4/metaphlan_databases/bowtie2_indexes you already have the bowtie2 indexes. You would just need to untar them and place them in the metaphlan_databases folder with the software or add an environment variable $METAPHLAN_DB_DIR that is set to the path to the folders.
Thank you,
Lauren
Hi @lauren.j.mciver
Thank you for your help.
I downloaded the database from Index of /biobakery4/metaphlan_databases/bowtie2_indexes and placed in inside the metaphlan_databse with the software itself.
But I am getting now this error
biobakery_workflows_databases --install wmgx
Installing humann utility mapping database
Creating directory to install database: /home/qiime2/biobakery_workflows_databases/humann
Creating subdirectory to install database: /home/qiime2/biobakery_workflows_databases/humann/utility_mapping
Download URL: http://huttenhower.sph.harvard.edu/humann_data/full_mapping_v201901b.tar.gz
Downloading file of size: 2.55 GB
2.55 GB 100.00 % 1.05 MB/sec 0 min -0 sec
Extracting: /home/qiime2/biobakery_workflows_databases/humann/full_mapping_v201901b.tar.gz
Database installed: /home/qiime2/biobakery_workflows_databases/humann/utility_mapping
HUMAnN configuration file updated: database_folders : utility_mapping = /home/qiime2/biobakery_workflows_databases/humann/utility_mapping
Unable to find strainphlan install.
I is quite frustrating, and I ma badly stuck into it
Kindly help out