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planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit 5bc9005790b78aabb615f559f31ee71c714c7072
author sanbi-uwc
date Wed, 12 Sep 2018 05:23:00 -0400
parents 0a66d41464b4
children
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0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
diff changeset
1 PLINK v1.90b3q 64-bit (29 May 2015)
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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2 Options in effect:
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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3 --bfile ACB_example
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
diff changeset
4 --chr 6
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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5 --make-bed
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
diff changeset
6 --out per_chrom/ACB_example_chr6
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
diff changeset
7
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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8 Hostname: MGH001803.local
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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9 Working directory: /Users/alicia/Dropbox/Shared/anc_sandbox
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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10 Start time: Sun Oct 4 10:47:54 2015
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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11
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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12 Random number seed: 1443970074
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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13 16384 MB RAM detected; reserving 8192 MB for main workspace.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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14 47613 variants loaded from .bim file.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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15 489 people (251 males, 238 females) loaded from .fam.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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16 Using 1 thread (no multithreaded calculations invoked).
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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17 Before main variant filters, 343 founders and 146 nonfounders present.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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18 Calculating allele frequencies... done.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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19 Total genotyping rate is 0.995496.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
diff changeset
20 47613 variants and 489 people pass filters and QC.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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21 Note: No phenotypes present.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
diff changeset
22 --make-bed to per_chrom/ACB_example_chr6.bed + per_chrom/ACB_example_chr6.bim +
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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23 per_chrom/ACB_example_chr6.fam ... done.
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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24
0a66d41464b4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit d75648a99156867f43b45dc4cdb6fdb12bfc5de4
sanbi-uwc
parents:
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25 End time: Sun Oct 4 10:47:54 2015