Issue #15 new
Former user created an issue

I am trying to run script but if fails message as below chintanlab@chintanlab-G41D3C[chintanlab] cd Desktop [ 6:13PM] chintanlab@chintanlab-G41D3C[Desktop] cd metaphlan [ 6:13PM] chintanlab@chintanlab-G41D3C[metaphlan] mkdir profiled_samples [ 6:13PM] mkdir: cannot create directory ‘profiled_samples’: File exists chintanlab@chintanlab-G41D3C[metaphlan] samples"SRS014459 SRS014464 SRS014470 SRS014494" zsh: command not found: samplesSRS014459 SRS014464 SRS014470 SRS014494 chintanlab@chintanlab-G41D3C[metaphlan] samples="SRS014459 SRS014464 SRS014470 SRS014494" chintanlab@chintanlab-G41D3C[metaphlan] for s in ${samples} [ 6:15PM] for> do for> tar xjfO input/${s}.tar.bz2 | python metaphlan.py --mpa_pkl db_v20/mpa_v20_m200.pkl --bowtie2db db_v20/mpa_v20_m200 --bt2_ps very-sensitive --input_type multifastq -t rel_ab --bowtie2out profiled_samples/${s}.bowtie2_out.bz2 -o profiled_samples/${s}.txt for> done tar (child): input/SRS014459 SRS014464 SRS014470 SRS014494.tar.bz2: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now usage: metaphlan.py [-h] [-v] [-t ANALYSIS TYPE] [--tax_lev TAXONOMIC_LEVEL] [--nreads NUMBER_OF_READS] [--pres_th PRESENCE_THRESHOLD] [--blastdb METAPHLAN_BLAST_DB] [--bowtie2db METAPHLAN_BOWTIE2_DB] [--evalue] [--word_size] [--bt2_ps BowTie2 presets] [--tmp_dir] [--min_cu_len] [--input_type {automatic,multifasta,multifastq,blastout,bowtie2out}] [--stat_q] [--blastn_exe BLASTN_EXE] [--bowtie2_exe BOWTIE2_EXE] [--blastout FILE_NAME] [--bowtie2out FILE_NAME] [--no_map] [-o output file] [--nproc N] [-biom biom_output] [-mdelim mdelim] [INPUT_FILE] [OUTPUT_FILE] metaphlan.py: error: unrecognized arguments: --mpa_pkl

Comments (0)

  1. Log in to comment