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Viewing changes to qiime_test_data/pick_open_reference_otus/ucrss_usearch/log_20130409153546.txt

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
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qiime_test_data/pick_open_reference_otus/ucrss_usearch/log_20130409153546.txt
 
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Logging started at 15:35:46 on 09 Apr 2013
 
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QIIME version: 1.6.0-dev
 
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qiime_config values:
 
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blastmat_dir    /Applications/blast-2.2.22/data/
 
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sc_queue        all.q
 
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topiaryexplorer_project_dir     /Users/caporaso/code/TopiaryExplorer-0.9.1/
 
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pynast_template_alignment_fp    /Users/caporaso/data/greengenes_core_sets/core_set_aligned_imputed.fasta_11_8_07.no_dots
 
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cluster_jobs_fp start_parallel_jobs.py
 
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assign_taxonomy_reference_seqs_fp       /Users/caporaso/data/gg_12_10_otus/rep_set/97_otus.fasta
 
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torque_queue    friendlyq
 
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template_alignment_lanemask_fp  /Users/caporaso/data/greengenes_core_sets/lanemask_in_1s_and_0s.txt
 
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jobs_to_start   2
 
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cloud_environment       False
 
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qiime_scripts_dir       /Users/caporaso/code/Qiime/scripts
 
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denoiser_min_per_core   50
 
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python_exe_fp   python
 
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temp_dir        /Users/caporaso/temp
 
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blastall_fp     blastall
 
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seconds_to_sleep        1
 
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assign_taxonomy_id_to_taxonomy_fp       /Users/caporaso/data/gg_12_10_otus/taxonomy/97_otu_taxonomy.txt
 
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parameter file values:
 
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align_seqs:min_length   75
 
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parallel:jobs_to_start  2
 
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pick_otus:enable_rev_strand_match       True
 
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Input file md5 sums:
 
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/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna: 094e424cf45cba69ef1c45fc7f61366f
 
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/Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna: facf235fdcd71d1e99048705276103ab
 
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Overridding similiary with 0.600.
 
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Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
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Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
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Executing commands.
 
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# Pick Reference OTUs (prefilter) command 
 
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pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//prefilter_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m usearch61_ref --similarity 0.6 --enable_rev_strand_match --suppress_new_clusters
 
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Stdout:
 
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Stderr:
 
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# Filter prefilter failures from input command 
 
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filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//prefilter_otus//prefiltered_seqs1.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//prefilter_otus//seqs1_failures.txt -n
 
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Stdout:
 
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Stderr:
 
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# Pick Reference OTUs command 
 
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pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//prefilter_otus//prefiltered_seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m usearch61_ref --enable_rev_strand_match --suppress_new_clusters
 
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Stdout:
 
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Stderr:
 
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# Generate full failures fasta file command 
 
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filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//prefilter_otus//prefiltered_seqs1.fna -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/prefiltered_seqs1_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/failures.fasta
 
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Stdout:
 
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Stderr:
 
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Forcing --suppress_new_clusters as this is reference-based OTU picking.
 
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Executing commands.
 
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# Pick rep set command 
 
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pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/prefiltered_seqs1_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/step1_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//prefilter_otus//prefiltered_seqs1.fna
 
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Stdout:
 
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Stderr:
 
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# Pick de novo OTUs for new clusters command 
 
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pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/subsampled_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step2_otus/ -m usearch61  --uclust_otu_id_prefix New.ReferenceOTU --enable_rev_strand_match
 
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Stdout:
 
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Stderr:
 
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# Pick representative set for subsampled failures command 
 
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pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step2_otus//subsampled_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step2_otus//step2_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/subsampled_failures.fasta
 
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Stdout:
 
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Stderr:
 
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# Pick reference OTUs using de novo rep set command 
 
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pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step3_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step2_otus//step2_rep_set.fna -m usearch61_ref --enable_rev_strand_match --suppress_new_clusters
 
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Stdout:
 
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Stderr:
 
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# Create fasta file of step3 failures command 
 
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filter_fasta.py -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/failures.fasta -s /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step3_otus//failures_failures.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step3_otus//failures_failures.fasta
 
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Stdout:
 
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Stderr:
 
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# Pick de novo OTUs on step3 failures command 
 
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pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step3_otus//failures_failures.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step4_otus/ -m usearch61  --uclust_otu_id_prefix New.CleanUp.ReferenceOTU --enable_rev_strand_match
 
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Stdout:
 
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Stderr:
 
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# Merge OTU maps command 
 
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cat /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step1_otus/prefiltered_seqs1_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step3_otus//failures_otus.txt /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step4_otus//failures_failures_otus.txt >> /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//final_otu_map.txt
 
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Stdout:
 
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Stderr:
 
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# Pick representative set for subsampled failures command 
 
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pick_rep_set.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step4_otus//failures_failures_otus.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step4_otus//step4_rep_set.fna -f /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//step3_otus//failures_failures.fasta
 
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Stdout:
 
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Stderr:
 
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Executing commands.
 
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# Make the otu table command 
 
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make_otu_table.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//final_otu_map_mc2.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//otu_table_mc2.biom
 
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Stdout:
 
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Stderr:
 
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Executing commands.
 
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# Assign taxonomy command 
 
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assign_taxonomy.py -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//rdp_assigned_taxonomy -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//rep_set.fna 
 
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Stdout:
 
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Stderr:
 
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Executing commands.
 
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# Add taxa to OTU table command 
 
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add_metadata.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//otu_table_mc2.biom --observation_mapping_fp /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//rdp_assigned_taxonomy/rep_set_tax_assignments.txt -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//otu_table_mc2_w_tax.biom --sc_separated taxonomy --observation_header OTUID,taxonomy
 
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Stdout:
 
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Stderr:
 
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Executing commands.
 
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# Align sequences command 
 
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align_seqs.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//rep_set.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//pynast_aligned_seqs --min_length 75
 
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Stdout:
 
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Stderr:
 
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# Filter alignment command 
 
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filter_alignment.py -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//pynast_aligned_seqs -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//pynast_aligned_seqs/rep_set_aligned.fasta 
 
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Stdout:
 
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Stderr:
 
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# Build phylogenetic tree command 
 
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make_phylogeny.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//pynast_aligned_seqs/rep_set_aligned_pfiltered.fasta -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//rep_set.tre 
 
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Stdout:
 
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Stderr:
 
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Executing commands.
 
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Logging stopped at 15:37:33 on 09 Apr 2013