Mercurial > repos > iuc > stacks_assembleperead

annotate test-data/ustacks/ustacks.out @ 13:38ecfb8d52c6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 22:02:47 +0000
parents e6919d8ae34d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
1 ustacks parameters selected:
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
2 Sample ID: 1
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
3 Min depth of coverage to create a stack: 2
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
4 Max distance allowed between stacks: 2
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
5 Max distance allowed to align secondary reads: 4
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
6 Max number of stacks allowed per de novo locus: 3
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
7 Deleveraging algorithm: disabled
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
8 Removal algorithm: enabled
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
9 Model type: SNP
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
10 Alpha significance level for model: 0.05
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
11 Gapped alignments: disabled
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
12 Parsing stacks_inputs/PopA_01.fq
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
13 Loading RAD-Tags...done
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
14 Loaded 66 RAD-Tags.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
15 Inserted 7 elements into the RAD-Tags hash map.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
16 0 reads contained uncalled nucleotides that were modified.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
17 4 initial stacks were populated; 3 stacks were set aside as secondary reads.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
18 Initial coverage mean: 15.75; Std Dev: 7.46241; Max: 27
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
19 Deleveraging trigger: 23; Removal trigger: 31
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
20 Calculating distance for removing repetitive stacks.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
21 Distance allowed between stacks: 1; searching with a k-mer length of 47 (48 k-mers per read); 1 k-mer hits required.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
22 Removing repetitive stacks.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
23 Removed 0 stacks.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
24 4 stacks remain for merging.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
25 Post-Repeat Removal, coverage depth Mean: 15.75; Std Dev: 7.46241; Max: 27
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
26 Calculating distance between stacks...
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
27 Distance allowed between stacks: 2; searching with a k-mer length of 31 (64 k-mers per read); 2 k-mer hits required.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
28 Merging stacks, maximum allowed distance: 2 nucleotide(s)
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
29 4 stacks merged into 3 loci; deleveraged 0 loci; blacklisted 0 loci.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
30 After merging, coverage depth Mean: 21; Std Dev: 4.24264; Max: 27
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
31 Merging remainder radtags
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
32 3 remainder sequences left to merge.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
33 Distance allowed between stacks: 4; searching with a k-mer length of 17 (78 k-mers per read); 10 k-mer hits required.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
34 Matched 3 remainder reads; unable to match 0 remainder reads.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
35 After remainders merged, coverage depth Mean: 22; Std Dev: 4.32049; Max: 28
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
36 Calling final consensus sequences, invoking SNP-calling model...
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
37 Number of utilized reads: 66
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
38 Writing loci, SNPs, and alleles to 'stacks_outputs/'...
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
39 Refetching sequencing IDs from stacks_inputs/PopA_01.fq... read 66 sequence IDs.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
40 done.
e6919d8ae34d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
diff changeset
41 ustacks is done.