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  • 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_de_novo_otus/otus/log_20120314213442.txt
 
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Logging started at 21:34:42 on 14 Mar 2012
 
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QIIME version: 1.4.0-dev, svn revision 2835
 
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qiime_config values:
 
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blastmat_dir    /Applications/blast-2.2.22/data/
 
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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 /Users/caporaso/code/Qiime/scripts/start_parallel_jobs.py
 
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assign_taxonomy_reference_seqs_fp       /Users/caporaso/data/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011.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        6
 
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assign_taxonomy_id_to_taxonomy_fp       /Users/caporaso/data/gg_otus_4feb2011/taxonomies/greengenes_tax_rdp_train.txt
 
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parameter file values:
 
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parallel:jobs_to_start  2
 
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Input file md5 sums:
 
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/Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/seqs.fna: e5e7fe1c3112f7655114702343c5fe54
 
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Executing commands.
 
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# Pick OTUs command 
 
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python /Users/caporaso/code/Qiime/scripts/pick_otus.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/seqs.fna -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//uclust_picked_otus 
 
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Stdout:
 
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Stderr:
 
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# Pick representative set command 
 
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python /Users/caporaso/code/Qiime/scripts/pick_rep_set.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//uclust_picked_otus/seqs_otus.txt -f /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/seqs.fna -l /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.log -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.fasta 
 
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Stdout:
 
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Stderr:
 
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# Assign taxonomy command 
 
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python /Users/caporaso/code/Qiime/scripts/assign_taxonomy.py -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rdp_assigned_taxonomy -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.fasta 
 
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Stdout:
 
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Stderr:
 
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# Make OTU table command 
 
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python /Users/caporaso/code/Qiime/scripts/make_otu_table.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//uclust_picked_otus/seqs_otus.txt -t /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//otu_table.biom 
 
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Stdout:
 
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Stderr:
 
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# Align sequences command 
 
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python /Users/caporaso/code/Qiime/scripts/align_seqs.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set//seqs_rep_set.fasta -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs 
 
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Stdout:
 
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Stderr:
 
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# Filter alignment command 
 
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python /Users/caporaso/code/Qiime/scripts/filter_alignment.py -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs/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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python /Users/caporaso/code/Qiime/scripts/make_phylogeny.py -i /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta -o /Users/caporaso/data/qiime_test_data/pick_otus_through_otu_table/otus//rep_set.tre 
 
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Stdout:
 
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Stderr:
 
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Logging stopped at 21:36:13 on 14 Mar 2012