MetaPhlAn: KeyError: 'mpa_mpa_v296_CHOCOPhlAn_201901.tar'

On a fresh conda install (`metaphlan 3.0 pyh5ca1d4c_1 bioconda) with python 3.6, nothing else in environment:

$ metaphlan --input_type fastq kneaddata/C0005_3F_1A_1000k_1_kneaddata.fastq -o ./

Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1
Downloading file of size: 0.00 MB
0.01 MB 232.33 %   4.76 MB/sec  0 min -0 sec
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes

File /home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan_databases/file_list.txt already present!
Traceback (most recent call last):
  File "/home/vklepacc/miniconda3/envs/metaphlan3/bin/metaphlan", line 10, in <module>
    sys.exit(main())
  File "/home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan.py", line 1187, in main
    pars['index'] = check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'], pars['force_download'])
  File "/home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan.py", line 610, in check_and_install_database
    download_unpack_tar(FILE_LIST, index, bowtie2_db, bowtie2_build, nproc)
  File "/home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan.py", line 463, in download_unpack_tar
    url_tar_file = ls_f["mpa_" + download_file_name + ".tar"]
KeyError: 'mpa_mpa_v296_CHOCOPhlAn_201901.tar'

About this issue

Original URL
State: closed
Created 4 years ago
Reactions: 1
Comments: 15 (5 by maintainers)

Most upvoted comments

I’ll bump a new conda build with the updates included in 3.0

Thank you for the advice, I’ll mention to checkout to the 3.0 in the manual

fbeghini on Apr 21, 2020

That’s strange, that bug was fixed in the second build, also it seems that conda installed the previous version, the latest build is

metaphlan 3.0 pyh5ca1d4c_2 bioconda

Francesco Beghini PhD Student

Lab. of Computational Metagenomics Department of Cellular, Computational and Integrative Biology - CIBIO University of Trento Via Sommarive 9, 38123 Trento, Italy

On Tue, Apr 7, 2020 at 4:13 PM Kevin Bonham notifications@github.com wrote:

On a fresh conda install (`metaphlan 3.0 pyh5ca1d4c_1 bioconda) with python 3.6, nothing else in environment:

$ metaphlan --input_type fastq kneaddata/C0005_3F_1A_1000k_1_kneaddata.fastq -o ./

Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1 Downloading file of size: 0.00 MB 0.01 MB 232.33 % 4.76 MB/sec 0 min -0 sec Downloading MetaPhlAn database Please note due to the size this might take a few minutes

File /home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan_databases/file_list.txt already present! Traceback (most recent call last): File “/home/vklepacc/miniconda3/envs/metaphlan3/bin/metaphlan”, line 10, in <module> sys.exit(main()) File “/home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 1187, in main pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’]) File “/home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 610, in check_and_install_database download_unpack_tar(FILE_LIST, index, bowtie2_db, bowtie2_build, nproc) File “/home/vklepacc/miniconda3/envs/metaphlan3/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 463, in download_unpack_tar url_tar_file = ls_f[“mpa_” + download_file_name + “.tar”] KeyError: ‘mpa_mpa_v296_CHOCOPhlAn_201901.tar’

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fbeghini on Apr 7, 2020