Closed smangul1 closed 8 years ago
python /u/home/s/serghei/code2/rop/tools/metaphlan2.py /u/home/s/serghei/code2/rop/example/metaphlan/lostHumanReads/unmappedExample_after_rRNA_lostHuman.fasta /u/home/s/serghei/code2/rop/example/metaphlan/microbiomeProfile//metaphlan/unmappedExample_metaphlan.map --mpl_pkl /u/home/s/serghei/code2/rop/db/metaphlan/mpa_v20_m200.pkl --input_type multifasta --bowtie2db /u/home/s/serghei/code2/rop/db/metaphlan/mpa_v20_m200 -t reads_map --nproc 8 --bowtie2out /u/home/s/serghei/code2/rop/example/metaphlan/microbiomeProfile//metaphlan/unmappedExample_bowtie2out.txt
Warning! Biom python library not detected! Exporting to biom format will not work! usage: metaphlan2.py --mpa_pkl MPA_PKL --input_type {fastq,fasta,multifasta,multifastq,bowtie2out,sam} [--bowtie2db METAPHLAN_BOWTIE2_DB] [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE] [--bowtie2out FILE_NAME] [--no_map] [--tmp_dir] [--tax_lev TAXONOMIC_LEVEL] [--min_cu_len] [--min_alignment_len] [--ignore_viruses] [--ignore_eukaryotes] [--ignore_bacteria] [--ignore_archaea] [--stat_q] [--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat] [-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS] [--pres_th PRESENCE_THRESHOLD] [--clade] [--min_ab] [-h] [-o output file] [--sample_id_key name] [--sample_id value] [-s sam_output_file] [--biom biom_output] [--mdelim mdelim] [--nproc N] [-v] [INPUT_FILE] [OUTPUT_FILE] metaphlan2.py: error: argument --mpa_pkl is required Warning! Biom python library not detected!
It works now.
harrydgnt
commented
8 years ago
python /u/home/s/serghei/code2/rop/tools/metaphlan2.py /u/home/s/serghei/code2/rop/example/metaphlan/lostHumanReads/unmappedExample_after_rRNA_lostHuman.fasta /u/home/s/serghei/code2/rop/example/metaphlan/microbiomeProfile//metaphlan/unmappedExample_metaphlan.map --mpl_pkl /u/home/s/serghei/code2/rop/db/metaphlan/mpa_v20_m200.pkl --input_type multifasta --bowtie2db /u/home/s/serghei/code2/rop/db/metaphlan/mpa_v20_m200 -t reads_map --nproc 8 --bowtie2out /u/home/s/serghei/code2/rop/example/metaphlan/microbiomeProfile//metaphlan/unmappedExample_bowtie2out.txt
python /u/home/s/serghei/code2/rop/tools/metaphlan2.py --mpl_pkl /u/home/s/serghei/code2/rop/db/metaphlan/mpa_v20_m200.pkl --input_type bowtie2out /u/home/s/serghei/code2/rop/example/metaphlan/microbiomeProfile//metaphlan/unmappedExample_bowtie2out.txt -t rel_ab > /u/home/s/serghei/code2/rop/example/metaphlan/microbiomeProfile//metaphlan/unmappedExample_metaphlan_output.tsv
Warning! Biom python library not detected! Exporting to biom format will not work! usage: metaphlan2.py --mpa_pkl MPA_PKL --input_type {fastq,fasta,multifasta,multifastq,bowtie2out,sam} [--bowtie2db METAPHLAN_BOWTIE2_DB] [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE] [--bowtie2out FILE_NAME] [--no_map] [--tmp_dir] [--tax_lev TAXONOMIC_LEVEL] [--min_cu_len] [--min_alignment_len] [--ignore_viruses] [--ignore_eukaryotes] [--ignore_bacteria] [--ignore_archaea] [--stat_q] [--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat] [-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS] [--pres_th PRESENCE_THRESHOLD] [--clade] [--min_ab] [-h] [-o output file] [--sample_id_key name] [--sample_id value] [-s sam_output_file] [--biom biom_output] [--mdelim mdelim] [--nproc N] [-v] [INPUT_FILE] [OUTPUT_FILE] metaphlan2.py: error: argument --mpa_pkl is required Warning! Biom python library not detected!