annotate test-data/denovo_map/denovo_map.log @ 0:b9822370f843 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:04:37 -0400
parents
children 421c33b8bf17
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
1 denovo_map.pl version 2.4 started at 2019-06-18 10:34:45
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
2 /home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
3
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
4 ustacks
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
5 ==========
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
6
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
7 Sample 1 of 2 'PopA_01'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
8 ----------
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
9 ustacks -t fastq -f demultiplexed/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
10 ustacks parameters selected:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
11 Input file: 'demultiplexed/PopA_01.1.fq'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
12 Sample ID: 1
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
13 Min depth of coverage to create a stack (m): 3
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
14 Repeat removal algorithm: enabled
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
15 Max distance allowed between stacks (M): 2
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
16 Max distance allowed to align secondary reads: 4
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
17 Max number of stacks allowed per de novo locus: 3
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
18 Deleveraging algorithm: disabled
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
19 Gapped assembly: enabled
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
20 Minimum alignment length: 0.8
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
21 Model type: SNP
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
22 Alpha significance level for model: 0.05
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
23
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
24 Loading RAD-Tags...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
25
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
26 Loaded 66 reads; formed:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
27 4 stacks representing 63 primary reads (95.5%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
28 3 secondary stacks representing 3 secondary reads (4.5%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
29
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
30 Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
31 Removing repetitive stacks: cov > 39 (mean+3*stdev)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
32 Blacklisted 0 stacks.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
33 Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
34
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
35 Assembling stacks (max. dist. M=2)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
36 Assembled 4 stacks into 3; blacklisted 0 stacks.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
37 Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
38
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
39 Merging secondary stacks (max. dist. N=4 from consensus)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
40 Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
41 Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
42
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
43 Assembling stacks, allowing for gaps (min. match length 80.0%)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
44 Assembled 3 stacks into 3 stacks.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
45 Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
46
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
47 Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
48 Merged 0 out of 0 secondary reads (-nan%).
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
49 Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
50
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
51 Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
52 Calling consensus sequences and haplotypes for catalog assembly...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
53 Writing tags, SNPs, and alleles files...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
54 Refetching read IDs...done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
55 ustacks is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
56
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
57 Sample 2 of 2 'PopA_02'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
58 ----------
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
59 ustacks -t fastq -f demultiplexed/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
60 ustacks parameters selected:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
61 Input file: 'demultiplexed/PopA_02.1.fq'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
62 Sample ID: 2
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
63 Min depth of coverage to create a stack (m): 3
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
64 Repeat removal algorithm: enabled
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
65 Max distance allowed between stacks (M): 2
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
66 Max distance allowed to align secondary reads: 4
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
67 Max number of stacks allowed per de novo locus: 3
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
68 Deleveraging algorithm: disabled
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
69 Gapped assembly: enabled
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
70 Minimum alignment length: 0.8
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
71 Model type: SNP
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
72 Alpha significance level for model: 0.05
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
73
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
74 Loading RAD-Tags...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
75
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
76 Loaded 60 reads; formed:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
77 4 stacks representing 55 primary reads (91.7%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
78 5 secondary stacks representing 5 secondary reads (8.3%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
79
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
80 Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
81 Removing repetitive stacks: cov > 42 (mean+3*stdev)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
82 Blacklisted 0 stacks.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
83 Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
84
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
85 Assembling stacks (max. dist. M=2)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
86 Assembled 4 stacks into 3; blacklisted 0 stacks.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
87 Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
88
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
89 Merging secondary stacks (max. dist. N=4 from consensus)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
90 Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
91 Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
92
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
93 Assembling stacks, allowing for gaps (min. match length 80.0%)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
94 Assembled 3 stacks into 3 stacks.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
95 Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
96
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
97 Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
98 Merged 0 out of 0 secondary reads (-nan%).
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
99 Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
100
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
101 Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
102 Calling consensus sequences and haplotypes for catalog assembly...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
103 Writing tags, SNPs, and alleles files...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
104 Refetching read IDs...done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
105 ustacks is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
106
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
107 Depths of Coverage for Processed Samples:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
108 PopA_01: 22.00x
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
109 PopA_02: 20.00x
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
110
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
111 cstacks
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
112 ==========
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
113 cstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
114
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
115 cstacks parameters selected:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
116 Loci matched based on sequence identity.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
117 Number of mismatches allowed between stacks: 1
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
118 Gapped alignments: enabled
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
119 Constructing catalog from 2 samples.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
120
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
121 Initializing new catalog...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
122 Parsing stacks_outputs/PopA_01.tags.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
123 Parsing stacks_outputs/PopA_01.snps.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
124 Parsing stacks_outputs/PopA_01.alleles.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
125 3 loci were newly added to the catalog.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
126
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
127 Processing sample stacks_outputs/PopA_02 [2 of 2]
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
128 Parsing stacks_outputs/PopA_02.tags.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
129 Parsing stacks_outputs/PopA_02.snps.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
130 Parsing stacks_outputs/PopA_02.alleles.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
131 Searching for sequence matches...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
132 3 loci in the catalog, 184 kmers in the catalog hash.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
133 Searching for gapped alignments...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
134 Merging matches into catalog...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
135 3 loci were matched to a catalog locus.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
136 0 loci were matched to a catalog locus using gapped alignments.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
137 0 loci were newly added to the catalog.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
138 0 loci matched more than one catalog locus, linking them.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
139 0 linked catalog loci were merged into 0 loci.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
140
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
141 Writing catalog in directory 'stacks_outputs/'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
142 Final catalog contains 3 loci.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
143 cstacks is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
144
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
145 sstacks
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
146 ==========
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
147 sstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
148
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
149 Searching for matches by sequence identity...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
150 Parsing stacks_outputs/catalog.tags.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
151 Parsing stacks_outputs/catalog.snps.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
152 Parsing stacks_outputs/catalog.alleles.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
153 Populating kmer dictionary for exact matches...done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
154 Populating kmer dictionary for gapped alignments...done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
155
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
156 Processing sample 'stacks_outputs/PopA_01' [1 of 2]
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
157 Parsing stacks_outputs/PopA_01.tags.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
158 Parsing stacks_outputs/PopA_01.snps.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
159 Parsing stacks_outputs/PopA_01.alleles.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
160 Searching for sequence matches...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
161 3 sample loci compared against the catalog containing 3 loci.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
162 3 matching loci, 0 contained no verified haplotypes.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
163 0 loci matched more than one catalog locus and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
164 0 loci contained SNPs unaccounted for in the catalog and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
165 4 total haplotypes examined from matching loci, 4 verified.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
166 Searching for gapped alignments...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
167 Out of 3 query loci, 0 gapped alignments attempted.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
168 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
169 0 loci matched no catalog locus;
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
170 0 loci matched more than one catalog locus and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
171 0 loci contained SNPs unaccounted for in the catalog and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
172 0 loci had no verified haplotypes.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
173 0 loci had inconsistent alignments to a catalog locus and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
174 Outputing to file stacks_outputs/PopA_01.matches.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
175
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
176 Processing sample 'stacks_outputs/PopA_02' [2 of 2]
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
177 Parsing stacks_outputs/PopA_02.tags.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
178 Parsing stacks_outputs/PopA_02.snps.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
179 Parsing stacks_outputs/PopA_02.alleles.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
180 Searching for sequence matches...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
181 3 sample loci compared against the catalog containing 3 loci.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
182 3 matching loci, 0 contained no verified haplotypes.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
183 0 loci matched more than one catalog locus and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
184 0 loci contained SNPs unaccounted for in the catalog and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
185 4 total haplotypes examined from matching loci, 4 verified.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
186 Searching for gapped alignments...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
187 Out of 3 query loci, 0 gapped alignments attempted.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
188 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
189 0 loci matched no catalog locus;
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
190 0 loci matched more than one catalog locus and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
191 0 loci contained SNPs unaccounted for in the catalog and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
192 0 loci had no verified haplotypes.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
193 0 loci had inconsistent alignments to a catalog locus and were excluded.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
194 Outputing to file stacks_outputs/PopA_02.matches.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
195
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
196 sstacks is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
197
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
198 tsv2bam
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
199 ==========
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
200 tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
201
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
202 Logging to 'stacks_outputs/tsv2bam.log'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
203 Configuration for this run:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
204 Stacks directory: 'stacks_outputs/'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
205 Population map: 'denovo_map/popmap_cstacks.tsv'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
206 Num. samples: 2
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
207 Paired-end reads directory: 'demultiplexed/'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
208
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
209 Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
210 Loading the catalog...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
211 Processing sample 'PopA_01'...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
212 Processing sample 'PopA_02'...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
213
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
214 Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
215 Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
216
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
217 tsv2bam is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
218
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
219 gstacks
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
220 ==========
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
221 gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
222
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
223 Logging to 'stacks_outputs/gstacks.log'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
224 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
225
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
226 Configuration for this run:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
227 Input mode: denovo
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
228 Population map: 'denovo_map/popmap_cstacks.tsv'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
229 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
230 Output to: 'stacks_outputs/'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
231 Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
232
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
233 Reading BAM headers...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
234 Processing all loci...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
235 20%...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
236 50%...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
237 100%
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
238
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
239 Attempted to assemble and align paired-end reads for 3 loci:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
240 0 loci had no or almost no paired-end reads (0.0%);
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
241 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
242 For the remaining 3 loci (100.0%), a paired-end contig was assembled;
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
243 Average contig size was 204.3 bp;
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
244 0 paired-end contigs overlapped the forward region (0.0%)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
245 Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
246 Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
247 252 were successfuly aligned (100.0%);
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
248 Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
249
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
250 Genotyped 3 loci:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
251 effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
252 mean number of sites per locus: 194.3
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
253 a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
254
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
255 gstacks is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
256
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
257 populations
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
258 ==========
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
259 populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
260
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
261 Logging to 'stacks_outputs/populations.log'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
262 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
263 populations parameters selected:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
264 Percent samples limit per population: 0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
265 Locus Population limit: 1
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
266 Percent samples overall: 0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
267 Minor allele frequency cutoff: 0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
268 Maximum observed heterozygosity cutoff: 1
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
269 Applying Fst correction: none.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
270 Pi/Fis kernel smoothing: off
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
271 Fstats kernel smoothing: off
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
272 Bootstrap resampling: off
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
273
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
274 Parsing population map...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
275 The population map contained 2 samples, 1 population(s), 1 group(s).
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
276 Working on 2 samples.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
277 Working on 1 population(s):
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
278 1: PopA_01, PopA_02
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
279 Working on 1 group(s) of populations:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
280 defaultgrp: 1
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
281
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
282 Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
283 Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
284 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
285 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
286
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
287 Processing data in batches:
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
288 * load a batch of catalog loci and apply filters
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
289 * compute SNP- and haplotype-wise per-population statistics
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
290 * write the above statistics in the output files
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
291 * export the genotypes/haplotypes in specified format(s)
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
292 More details in 'stacks_outputs/populations.log.distribs'.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
293 Now processing...
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
294 Batch 1
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
295
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
296 Removed 0 loci that did not pass sample/population constraints from 3 loci.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
297 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
298 Number of loci with PE contig: 3.00 (100.0%);
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
299 Mean length of loci: 194.33bp (stderr 0.33);
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
300 Number of loci with SE/PE overlap: 0.00 (0.0%);
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
301 Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
302 Mean genotyped sites per locus: 194.33bp (stderr 0.33).
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
303
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
304 Population summary statistics (more detail in populations.sumstats_summary.tsv):
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
305 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
306 Populations is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
307 denovo_map.pl is done.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
308
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
309 denovo_map.pl completed at 2019-06-18 10:34:45