Mercurial > repos > iuc > stacks2_shortreads
annotate test-data/gstacks/gstacks.log.distribs @ 7:c287418eb288 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
author | iuc |
---|---|
date | Mon, 23 May 2022 17:48:31 +0000 |
parents | 17d39bf0a63a |
children |
rev | line source |
---|---|
0
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
1 # Note: Individual distributions can be extracted using the `stacks-dist-extract` utility. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
2 # e.g. `stacks-dist-extract gstacks.log.distribs dist_name` |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
3 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
4 BEGIN effective_coverages_per_sample |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
5 # For mean_cov_ns, the coverage at each locus is weighted by the number of |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
6 # samples present at that locus (i.e. coverage at shared loci counts more). |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
7 sample n_loci n_used_fw_reads mean_cov mean_cov_ns |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
8 PopA_01 3 96 32.000 32.000 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
9 PopA_02 3 90 30.000 30.000 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
10 END effective_coverages_per_sample |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
11 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
12 BEGIN phasing_rates_per_sample |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
13 sample n_gts n_multisnp_hets n_phased misphasing_rate |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
14 PopA_01 3 2 2 0.000 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
15 PopA_02 3 3 3 0.000 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
16 END phasing_rates_per_sample |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
17 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
18 BEGIN clockings |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
19 Num. threads: 1 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
20 Parallel time: 0.0 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
21 Average thread time spent: |
4
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
22 0.0 reading (2.8%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
23 0.0 processing (95.9%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
24 0.0 pre-alignments block (76.1%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
25 0.0 reformatting fw-reads (0.1%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
26 0.0 assembling (17.5%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
27 0.0 initializing alignments (4.0%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
28 0.0 aligning (52.9%) |
2
43e3eeb2e0ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
0
diff
changeset
|
29 0.0 merging read pairs (1.6%) |
4
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
30 0.0 post-alignments block (18.7%) |
0
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
31 0.0 filtering reads (0.0%) |
4
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
32 0.0 counting nucleotides (2.8%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
33 0.0 genotyping (1.2%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
34 0.0 haplotyping (1.0%) |
0
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
35 0.0 computing consensus (0.1%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
36 0.0 building_fa (0.1%) |
4
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
37 0.0 building_vcf (13.4%) |
2
43e3eeb2e0ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
0
diff
changeset
|
38 0.0 writing_fa (0.0%) |
43e3eeb2e0ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
0
diff
changeset
|
39 0.0 writing_vcf (0.9%) |
4
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
40 0.0 clocking (0.2%) |
17d39bf0a63a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
41 Total time spent writing vcf: 0.0 (0.9%) |
0
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
42 VCFwrite block size: mean=1.0(n=3); max=1 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
43 END clockings |