Error in profiling a single metagenome from raw reads

[sjtu-piaopiao]

Hi, I'm new to metaphlan, and trying to run the tutorial. But there was a problem with the first step. Code: metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta -o SRS014476-Supragingival_plaque_profile.txt Output: Warning! Biom python library not detected! Exporting to biom format will not work! Downloading MetaPhlAn database Please note due to the size this might take a few minutes File /lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.tar already present! File /lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.md5 already present! Traceback (most recent call last): File "/lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/bin/metaphlan", line 10, in sys.exit(main()) File "/lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan.py", line 985, in main pars['index'] = check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'], pars['force_download']) File "/lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/lib/python3.7/site-packages/metaphlan/init.py", line 304, in check_and_install_database download_unpack_tar(index, bowtie2_db, bowtie2_build, nproc, use_zenodo) File "/lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/lib/python3.7/site-packages/metaphlan/init.py", line 180, in download_unpack_tar bt2_build_output = subp.check_output([bowtie2_build, '--usage'], stderr=subp.STDOUT) File "/lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/lib/python3.7/subprocess.py", line 411, in check_output **kwargs).stdout File "/lustre/home/acct-clslt/clslt-pp/.conda/envs/mpa/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['bowtie2-build', '--usage']' returned non-zero exit status 127.

How can I solve this problem?

[kescobo]

Hi there! You may want to ask in the forums to get a quicker response: https://forum.biobakery.org/