Mercurial > repos > bgruening > salmon

annotate test-data/cached_locally/prebuilt_index/ref_indexing.log @ 15:cc05793bb896 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
author bgruening
date Sat, 03 Oct 2020 18:22:45 +0000
parents b265be7af3db
children
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b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
1 [2020-07-09 14:16:39.484] [puff::index::jointLog] [info] Running fixFasta
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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2 [2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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3 [2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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4 [2020-07-09 14:16:39.491] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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5 [2020-07-09 14:16:39.494] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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6 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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7 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory foo
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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8 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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9 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] contig count for validation: 23
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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10 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of Contigs : 23
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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11 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of numerical Contigs : 23
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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12 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Total # of contig vec entries: 36
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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13 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] bits per offset entry 6
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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14 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Done constructing the contig vector. 24
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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15 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] # segments = 23
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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16 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] total length = 19,592
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
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17 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Reading the reference files ...
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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diff changeset
18 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] positional integer width = 15
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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19 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] seqSize = 19,592
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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20 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] rankSize = 19,592
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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21 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] edgeVecSize = 0
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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22 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] num keys = 18,902
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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23 [2020-07-09 14:16:39.614] [puff::index::jointLog] [info] mphf size = 0.0125198 MB
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
24 [2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk size = 9,796
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
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25 [2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk 0 = [0, 9,796)
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
26 [2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562)
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
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27 [2020-07-09 14:16:39.618] [puff::index::jointLog] [info] finished populating pos vector
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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28 [2020-07-09 14:16:39.618] [puff::index::jointLog] [info] writing index components
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
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29 [2020-07-09 14:16:39.619] [puff::index::jointLog] [info] finished writing dense pufferfish index