Mercurial > repos > bgruening > alevin

annotate test-data/cached_locally/prebuilt_index/ref_indexing.log @ 9:ecb9ea6269ee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit fe9dd99a14770b6c5f26e24893599acb577e304f"
author bgruening
date Wed, 24 Mar 2021 20:15:12 +0000
parents 53d74155bb52
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
53d74155bb52 "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
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
2 [2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
3 [2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
4 [2020-07-09 14:16:39.491] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
5 [2020-07-09 14:16:39.494] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
6 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
7 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory foo
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
8 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
9 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] contig count for validation: 23
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
10 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of Contigs : 23
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
11 [2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of numerical Contigs : 23
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
12 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Total # of contig vec entries: 36
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
13 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] bits per offset entry 6
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
14 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Done constructing the contig vector. 24
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
15 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] # segments = 23
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
16 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] total length = 19,592
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
17 [2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Reading the reference files ...
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
18 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] positional integer width = 15
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
19 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] seqSize = 19,592
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
20 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] rankSize = 19,592
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
21 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] edgeVecSize = 0
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
22 [2020-07-09 14:16:39.548] [puff::index::jointLog] [info] num keys = 18,902
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
23 [2020-07-09 14:16:39.614] [puff::index::jointLog] [info] mphf size = 0.0125198 MB
53d74155bb52 "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
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
25 [2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk 0 = [0, 9,796)
53d74155bb52 "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)
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
27 [2020-07-09 14:16:39.618] [puff::index::jointLog] [info] finished populating pos vector
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
28 [2020-07-09 14:16:39.618] [puff::index::jointLog] [info] writing index components
53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents:
diff changeset
29 [2020-07-09 14:16:39.619] [puff::index::jointLog] [info] finished writing dense pufferfish index