I’m trying to install fastp, bowtie2, humann, and metaphlan. In a new conda environment created with python 3.7, I’ve configured the channels (as per the humann install instructions) and installed fastp, bowtie2, humann, and metaphlan.
The “metaphlan --install” command, however, has been stuck on “Building Bowtie2 indexes” for days.
I thought maybe it had built the indexes and my command line output was just stuck, but when I try to run metaphlan with
metaphlan datasets/yachida_crc/tmp_out/DRR127481.fasta.gz --input_type fasta
I get an error:
“No MetaPhlAn BowTie2 database found (–index option)!
Expecting location bowtie2db”
Below is the output of the command “metaphlan --install”:
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Downloading file of size: 0.00 MB
0.01 MB 25600.00 % 49.20 MB/sec 0 min -0 sec
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103.tar
Downloading file of size: 2623.07 MB
2623.07 MB 100.00 % 0.35 MB/sec 0 min -0 sec
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103.md5
Downloading file of size: 0.00 MB
0.01 MB 11702.86 % 49.42 MB/sec 0 min -0 sec
Decompressing /Users/jendawk/miniconda3/envs/bioenv2/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_VSG.fna.bz2 into /Users/jendawk/miniconda3/envs/bioenv2/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_VSG.fna
Decompressing /Users/jendawk/miniconda3/envs/bioenv2/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.fna.bz2 into /Users/jendawk/miniconda3/envs/bioenv2/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.fna
Joining FASTA databases
Building Bowtie2 indexes