Hi,
I’m following the tutorial here and having an issue at the step 3:
$ strainphlan -s consensus_markers_6A/.pkl -m clade_markers_6A/s__Bacteroides_vulgatus.fna -r reference_genomes/.fna -o output_6A -n 8 -c s__Bacteroides_vulgatus --phylophlan_mode fast --nproc 4
Mon Aug 31 23:19:26 2020: Start StrainPhlAn 3.0 execution
Mon Aug 31 23:19:26 2020: Creating temporary directory…
Mon Aug 31 23:19:26 2020: Done.
Mon Aug 31 23:19:26 2020: Getting markers from main sample files…
Mon Aug 31 23:19:26 2020: Done.
Mon Aug 31 23:19:26 2020: Getting markers from main reference files…
Mon Aug 31 23:19:27 2020: Done.
Mon Aug 31 23:19:27 2020: Removing bad markers / samples…
Mon Aug 31 23:19:27 2020: Done.
Mon Aug 31 23:19:27 2020: Writing samples as markers’ FASTA files…
Mon Aug 31 23:19:27 2020: Done.
Mon Aug 31 23:19:27 2020: Writing filtered clade markers as FASTA file…
Mon Aug 31 23:19:27 2020: Done.
Mon Aug 31 23:19:27 2020: Calculating polymorphic rates…
Mon Aug 31 23:19:27 2020: Done.
Mon Aug 31 23:19:27 2020: Executing PhyloPhlAn 3.0…
Mon Aug 31 23:19:27 2020: Creating PhyloPhlAn 3.0 database…
Mon Aug 31 23:19:27 2020: Done.
Mon Aug 31 23:19:27 2020: Generating PhyloPhlAn 3.0 configuration file…
Mon Aug 31 23:19:27 2020: Done.
Mon Aug 31 23:19:27 2020: Processing samples…
[e] Command ‘[’/opt/anaconda3/envs/metaphlan-3.0/bin/makeblastdb’, ‘-parse_seqids’, ‘-dbtype’, ‘nucl’, ‘-in’, ‘output_6A/tmpedq7rt4k/s__Bacteroides_vulgatus/s__Bacteroides_vulgatus.fna’, ‘-out’, ‘output_6A/tmpedq7rt4k/s__Bacteroides_vulgatus/s__Bacteroides_vulgatus’]’ returned non-zero exit status 1.
[e] cannot execute command
- command_line: /opt/anaconda3/envs/metaphlan-3.0/bin/makeblastdb -parse_seqids -dbtype nucl -in output_6A/tmpedq7rt4k/s__Bacteroides_vulgatus/s__Bacteroides_vulgatus.fna -out output_6A/tmpedq7rt4k/s__Bacteroides_vulgatus/s__Bacteroides_vulgatus*
-
stdin: None* -
stdout: None* -
env: {'TERM_PROGRAM': 'Apple_Terminal', 'SHELL': '/bin/bash', 'TERM': 'xterm-256color', 'TMPDIR': '/var/folders/tt/t3zlksc51kz4t1hrfzz9sfg80000gn/T/', 'CONDA_SHLVL': '2', 'CONDA_PROMPT_MODIFIER': '(metaphlan-3.0) ', 'TERM_PROGRAM_VERSION': '433', 'TERM_SESSION_ID': '8EA4A4B7-8CF4-4B7A-9F2E-FEF1AEE107E3', 'USER': 'sijiyeon', 'CONDA_EXE': '/opt/anaconda3/bin/conda', 'SSH_AUTH_SOCK': '/private/tmp/com.apple.launchd.qxFgVtcqtU/Listeners', '__CF_USER_TEXT_ENCODING': '0x1F5:0x0:0x0', '_CE_CONDA': '', 'CONDA_PREFIX_1': '/opt/anaconda3', 'PATH': '/opt/anaconda3/envs/metaphlan-3.0/bin:/opt/anaconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.8/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/sijiyeon/blast-2.2.22/bin:/Users/sijiyeon/seqtk:/Users/sijiyeon/Gblocks_0.91b:/Users/sijiyeon/graphlan:/opt/anaconda3/bin/bowtie2:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin', 'LaunchInstanceID': '30E02370-A829-436E-A3F3-8BD36D6C7D9D', '_': '/opt/anaconda3/envs/metaphlan-3.0/bin/strainphlan', 'CONDA_PREFIX': '/opt/anaconda3/envs/metaphlan-3.0', 'PWD': '/Users/sijiyeon/Dropbox/---201701_b.vulg_data_analysis/02_2_Bvul_highfat_pooled_shotgun/fastq', 'XPC_FLAGS': '0x0', '_CE_M': '', 'XPC_SERVICE_NAME': '0', 'SHLVL': '1', 'HOME': '/Users/sijiyeon', '__KMP_REGISTERED_LIB_4785': '0x10d3fe168-cafeaf19-libomp.dylib', 'CONDA_PYTHON_EXE': '/opt/anaconda3/bin/python', 'LOGNAME': 'sijiyeon', 'LC_CTYPE': 'UTF-8', 'CONDA_DEFAULT_ENV': 'metaphlan-3.0', 'DISPLAY': '/private/tmp/com.apple.launchd.tBb97xkeae/org.macosforge.xquartz:0', 'SECURITYSESSIONID': '186a6', 'JAVA_HOME8': '/Library/Java/JavaVirtualMachines/jdk-12.0.2.jdk/Contents/Home'}*
[e] An error was ocurred executing a external tool, exiting…
This is how I installed metaphylan (installed today):
conda create -n metaphlan-3.0 python=3.7
conda activate metaphlan-3.0 && conda install metaphlan=3.0.3
And my phylophylan version is:
PhyloPhlAn version 3.0.51 (11 May 2020)
What could be the possible cause? Thank you already!
