Mercurial > repos > iuc > plink

annotate test-data/plink_log.txt @ 0:a98caf1d69ab draft

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/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
author iuc
date Mon, 21 Sep 2020 10:09:22 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
1 PLINK v1.90p 64-bit (16 Jun 2020)
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
2 Options in effect:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
3 --bfile plink_input/plink_input
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
4 --indep-pairwise 50 5 0.2
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
5 --make-bed
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
6 --out plink_output/plink_output
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
7
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
8 Hostname: p-body.local
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
9 Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmpzq_so7fd/job_working_directory/000/90/working
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
10 Start time: Tue Sep 15 12:47:24 2020
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
11
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
12 Random number seed: 1600199244
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
13 32768 MB RAM detected; reserving 16384 MB for main workspace.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
14 50 variants loaded from .bim file.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
15 200 people (0 males, 200 females) loaded from .fam.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
16 200 phenotype values loaded from .fam.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
17 Using 1 thread (no multithreaded calculations invoked).
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
18 Before main variant filters, 200 founders and 0 nonfounders present.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
19 Calculating allele frequencies... done.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
20 50 variants and 200 people pass filters and QC.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
21 Among remaining phenotypes, 101 are cases and 99 are controls.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
22 --make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim +
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
23 plink_output/plink_output.fam ... done.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
24 Pruned 0 variants from chromosome 1, leaving 50.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
25 Pruning complete. 0 of 50 variants removed.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
26 Marker lists written to plink_output/plink_output.prune.in and
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
27 plink_output/plink_output.prune.out .
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
28
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff changeset
29 End time: Tue Sep 15 12:47:24 2020