Mercurial > repos > iuc > stacks_pstacks

annotate test-data/ustacks/ustacks.out @ 12:a9ff3d0184b8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 22:01:24 +0000
parents f42f9ae6d109
children
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8
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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diff changeset
1 ustacks parameters selected:
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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2 Sample ID: 1
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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3 Min depth of coverage to create a stack: 2
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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4 Max distance allowed between stacks: 2
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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5 Max distance allowed to align secondary reads: 4
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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6 Max number of stacks allowed per de novo locus: 3
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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7 Deleveraging algorithm: disabled
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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8 Removal algorithm: enabled
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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9 Model type: SNP
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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10 Alpha significance level for model: 0.05
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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11 Gapped alignments: disabled
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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12 Parsing stacks_inputs/PopA_01.fq
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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13 Loading RAD-Tags...done
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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14 Loaded 66 RAD-Tags.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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15 Inserted 7 elements into the RAD-Tags hash map.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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16 0 reads contained uncalled nucleotides that were modified.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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17 4 initial stacks were populated; 3 stacks were set aside as secondary reads.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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18 Initial coverage mean: 15.75; Std Dev: 7.46241; Max: 27
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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19 Deleveraging trigger: 23; Removal trigger: 31
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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20 Calculating distance for removing repetitive stacks.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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21 Distance allowed between stacks: 1; searching with a k-mer length of 47 (48 k-mers per read); 1 k-mer hits required.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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22 Removing repetitive stacks.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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23 Removed 0 stacks.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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24 4 stacks remain for merging.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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25 Post-Repeat Removal, coverage depth Mean: 15.75; Std Dev: 7.46241; Max: 27
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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26 Calculating distance between stacks...
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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27 Distance allowed between stacks: 2; searching with a k-mer length of 31 (64 k-mers per read); 2 k-mer hits required.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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28 Merging stacks, maximum allowed distance: 2 nucleotide(s)
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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29 4 stacks merged into 3 loci; deleveraged 0 loci; blacklisted 0 loci.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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30 After merging, coverage depth Mean: 21; Std Dev: 4.24264; Max: 27
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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31 Merging remainder radtags
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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32 3 remainder sequences left to merge.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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33 Distance allowed between stacks: 4; searching with a k-mer length of 17 (78 k-mers per read); 10 k-mer hits required.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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34 Matched 3 remainder reads; unable to match 0 remainder reads.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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35 After remainders merged, coverage depth Mean: 22; Std Dev: 4.32049; Max: 28
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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36 Calling final consensus sequences, invoking SNP-calling model...
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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37 Number of utilized reads: 66
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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38 Writing loci, SNPs, and alleles to 'stacks_outputs/'...
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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39 Refetching sequencing IDs from stacks_inputs/PopA_01.fq... read 66 sequence IDs.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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40 done.
f42f9ae6d109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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41 ustacks is done.