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error in biobakery_workflow_database #21

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Muneer111 opened this issue Aug 8, 2023 · 0 comments
Open

error in biobakery_workflow_database #21

Muneer111 opened this issue Aug 8, 2023 · 0 comments

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@Muneer111
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Muneer111 commented Aug 8, 2023

Hi@abmiguez
in hope you are fine,
I am trying to install biobakery an i am getting this error
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

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