Unable to download the CHOCOPhlAnSGB.md5 and other dataset

Microbial community profiling MetaPhlAn
1

The Error message:
$ metaphlan SRS014459-Stool.fasta.gz --input_type fasta --nproc 10 > SRS014459-Stool_profile.txt
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 25600.00 % 66.20 MB/sec 0 min -0 sec
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_vJun23_CHOCOPhlAnSGB_202403_bt2.tar
Downloading file of size: 21924.74 MB
21924.74 MB 100.00 % 0.99 MB/sec 0 min -0 sec
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJun23_CHOCOPhlAnSGB_202403_bt2.md5
Downloading file of size: 0.00 MB
/usr/lib64/python3.9/tarfile.py:2239: RuntimeWarning: The default behavior of tarfile extraction has been changed to disallow common exploits (including CVE-2007-4559). By default, absolute/parent paths are disallowed and some mode bits are cleared. See Mitigation of directory traversal attack in the Python tarfile library (CVE-2007-4559) - Red Hat Customer Portal for more details.
warnings.warn(
Warning: Unable to extract /home/kaop/research_proj/py_research/lib64/python3.9/site-packages/metaphlan/metaphlan_databases/mpa_vJun23_CHOCOPhlAnSGB_202403_bt2.tar.

Downloading and uncompressing additional files

Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJun23_CHOCOPhlAnSGB_202403.tar
Downloading file of size: 3162.71 MB
66.31 MB 2.10 % 2.11 MB/sec 24 min 26 sec
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJun23_CHOCOPhlAnSGB_202403.tar

Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJun23_CHOCOPhlAnSGB_202403.md5
Downloading file of size: 0.00 MB
0.01 MB 11702.86 % 110.33 MB/sec 0 min -0 sec
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJun23_CHOCOPhlAnSGB_202403.md5
MD5 checksums not found, something went wrong!

Hello, I took around 5 hours to work on this and it ended up such error message and only finished the first file downloading. I still have no idea why. I used Spartan (Cloud computing) to install it. Thanks

2

Hi @Edward_Kao

It seems like a security update was introduced at some point in python which disallows potentially dangerous tarball extraction patterns and you are using a version with this update. Would it be possible in your system to use a conda environment with metaphlan installed, so that you can be sure to use a version without this update?