Metaphlan2 install stuck at bowtie2 indexing?

[XT]

Hi, I used bioconda to install metaphlan2 version 2.9.21. I ran the metaphlan2.py --install --index mpa_v29_CHOCOPhlAn_201901 command, and it successfully downloads and decompresses the marker file. It the says "Building Bowtie2 indexes" and makes four .bt2 files in the metaphlan_databases directory within ~15 minutes but then seems to hang for days without completing or changing any additional files. Is it supposed to take forever, or is the process stuck? 

The process bowtie2-build-s is still active but not using any CPU (1% now vs 99% when it was first started). The 4 files in the directory are:

mpa_v29_CHOCOPhlAn_201901.1.bt2 - 25 MB

mpa_v29_CHOCOPhlAn_201901.2.bt2 - 0 bytes

mpa_v29_CHOCOPhlAn_201901.3.bt2 - 14.1 MB

mpa_v29_CHOCOPhlAn_201901.4.bt2 - 418.2 MB

Is this the correct number and size of bowtie2 index files?

Thanks,

Xiao

[Francesco Beghini]

Hi Xiao,

have you tried with the latest version of the MetaPhlAn2 software (2.9.5) and database ( mpa_v294_CHOCOPhlAn_201901)?

You can try to build the BowTie2 indexes by running bowtie2-build without the --quiet parameter in order to see in which stage the process is stuck

bowtie2-build mpa_v294_CHOCOPhlAn_201901.fna mpa_v294_CHOCOPhlAn_201901

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

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