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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_closed_reference_otus/otus_usearch/usearch_ref_picked_otus/usearch_cluster_err_corrected.log
 
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usearch --cluster /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch/usearch_ref_picked_otus/abundance_sorted.fasta --consout /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch/usearch_ref_picked_otus/clustered_error_corrected.fasta --usersort --id 0.97 --slots 16769023 --sizeout --uc /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch/usearch_ref_picked_otus/err_corrected_clusters.uc --w 12 --maxrejects 500 --sizein --log /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch/usearch_ref_picked_otus/usearch_cluster_err_corrected.log
 
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Started Thu Apr  4 08:05:52 2013
 
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Version 5.2.236
 
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17Gb RAM
 
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Hash size 16769023 (16.8M)
 
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Algorithm:
 
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  De novo clustering
 
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  Fast search (U-sorting) enabled
 
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  Similarity computed from a global alignment
 
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Word-counting heuristics:
 
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  Word length for database index 12
 
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  Step words 8
 
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  Bump fraction 50%
 
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U-sorted search termination:
 
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  Max accepts 1
 
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  Max rejects 500
 
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  Word count rejection enabled
 
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Accept criteria:
 
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  Min id 97.0%
 
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Query set:
 
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  Filename /Users/caporaso/code/Qiime/qiime_test_data/pick_reference_otus_through_otu_table/otus_usearch/usearch_ref_picked_otus/abundance_sorted.fasta
 
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  File size 283.2kb
 
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  Sequence type nucelotide
 
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Database:
 
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  Initially empty
 
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Substitution scores:
 
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  Match score 1.0
 
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  Mismatch score -2.0
 
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Gap penalties:
 
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     10.00  Open penalty (internal gaps)
 
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      0.50  Open penalty (end gaps)
 
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      1.00  Ext. penalty (internal gaps)
 
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      0.50  Ext. penalty (end gaps)
 
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Fast alignment heuristics:
 
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  HSP seed word length 5
 
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  One-hit HSP seeding
 
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  Exact word seeds (neighborhoods disabled)
 
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  Min HSP length 32
 
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  Band radius 16
 
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00:01 285Mb Result: 418 clusters, avg size 2.1, avg id. 98.8%
 
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Search time         1.00s
 
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Throughput          879.0 seqs/sec
 
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Query sequences     879
 
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Clusters            418
 
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Avg cluster size    2.1 seqs
 
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Avg cluster id      98.8%
 
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              Id      Allocs       Frees     Pct         Bytes
 
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----------------  ----------  ----------  ------  ------------
 
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           seqdb         839           0   84.1%          21Mb
 
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           cons2        5437           0    8.5%         2.1Mb
 
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           ultra          25           0    4.7%         1.2Mb
 
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            mx_h        1530        1032    1.4%       350.1kb
 
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          windex        4624         255    0.6%       141.5kb
 
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         myutils           4           0    0.5%       128.0kb
 
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       hspfinder         398         199    0.2%        45.3kb
 
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        comppath           1           0    0.0%       4335.0b
 
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           dpmem           4           2    0.0%       2184.0b
 
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----------------  ----------  ----------  ------  ------------
 
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           Total       12862        1488  100.0%          25Mb
 
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Finished Thu Apr  4 08:05:53 2013
 
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Elapsed time 00:01
 
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Max memory 285Mb