[2022-05-27 08:21:55.261] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:21:55.746] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:21:55.746] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:21:55.795] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:21:55.931] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:22:05.542] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:22:05.542] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:22:05.565] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:22:05.566] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:22:05.587] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:22:05.587] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:22:05.589] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:22:05.589] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:22:05.593] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:22:05.605] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:22:05.605] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:22:05.614] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:22:05.688] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:22:05.688] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:22:05.688] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:22:05.688] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:22:05.688] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:22:06.566] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:22:06.580] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:22:06.580] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:22:06.580] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:22:07.674] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:22:07.674] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:22:07.706] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 08:27:23.675] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:27:24.137] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:27:24.137] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:27:24.186] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:27:24.317] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:27:33.522] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:27:33.522] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:27:33.545] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:27:33.546] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:27:33.566] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:27:33.566] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:27:33.569] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:27:33.569] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:27:33.572] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:27:33.586] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:27:33.586] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:27:33.595] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:27:33.691] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:27:33.691] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:27:33.691] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:27:33.691] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:27:33.691] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:27:34.462] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:27:34.472] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:27:34.472] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:27:34.472] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:27:35.509] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:27:35.509] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:27:35.557] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 08:28:21.820] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:28:22.278] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:28:22.278] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:28:22.329] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:28:22.459] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:28:32.083] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:28:32.083] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:28:32.106] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:28:32.107] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:28:32.127] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:28:32.128] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:28:32.130] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:28:32.130] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:28:32.134] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:28:32.147] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:28:32.147] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:28:32.155] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:28:32.250] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:28:32.250] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:28:32.250] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:28:32.250] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:28:32.250] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:28:33.037] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:28:33.047] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:28:33.047] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:28:33.047] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:28:34.136] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:28:34.136] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:28:34.187] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 08:43:48.134] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:43:48.611] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:43:48.611] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:43:48.661] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:43:48.791] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:43:58.482] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:43:58.482] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:43:58.506] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:43:58.506] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:43:58.526] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:43:58.526] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:43:58.529] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:43:58.529] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:43:58.532] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:43:58.546] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:43:58.546] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:43:58.555] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:43:58.629] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:43:58.629] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:43:58.629] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:43:58.629] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:43:58.629] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:43:59.430] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:43:59.440] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:43:59.441] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:43:59.441] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:44:00.543] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:44:00.543] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:44:00.594] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 08:50:10.865] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:50:11.330] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:50:11.330] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:50:11.379] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:50:11.509] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:50:20.699] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:50:20.699] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:50:20.723] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:50:20.723] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:50:20.744] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:50:20.744] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:50:20.746] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:50:20.746] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:50:20.750] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:50:20.764] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:50:20.764] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:50:20.773] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:50:20.847] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:50:20.847] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:50:20.847] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:50:20.847] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:50:20.847] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:50:21.627] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:50:21.637] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:50:21.637] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:50:21.637] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:50:22.693] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:50:22.693] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:50:22.744] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 08:51:41.662] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:51:42.146] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:51:42.146] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:51:42.195] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:51:42.324] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:51:51.504] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:51:51.504] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:51:51.527] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:51:51.527] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:51:51.547] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:51:51.547] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:51:51.550] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:51:51.550] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:51:51.553] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:51:51.566] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:51:51.566] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:51:51.574] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:51:51.649] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:51:51.649] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:51:51.649] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:51:51.649] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:51:51.649] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:51:52.427] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:51:52.439] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:51:52.439] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:51:52.439] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:51:53.475] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:51:53.476] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:51:53.525] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 08:53:32.562] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:53:33.035] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:53:33.035] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:53:33.103] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:53:33.232] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:53:42.784] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:53:42.784] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:53:42.807] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:53:42.807] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:53:42.828] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:53:42.828] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:53:42.830] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:53:42.830] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:53:42.834] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:53:42.847] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:53:42.847] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:53:42.855] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:53:42.934] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:53:42.934] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:53:42.934] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:53:42.934] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:53:42.934] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:53:43.725] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:53:43.736] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:53:43.736] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:53:43.736] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:53:44.821] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:53:44.821] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:53:44.873] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 08:54:31.696] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 08:54:32.176] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 08:54:32.176] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 08:54:32.227] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 08:54:32.357] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 08:54:41.958] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 08:54:41.958] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 08:54:41.982] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 08:54:41.982] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 08:54:42.003] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 08:54:42.003] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 08:54:42.005] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 08:54:42.005] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 08:54:42.008] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 08:54:42.022] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 08:54:42.022] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 08:54:42.031] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 08:54:42.110] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 08:54:42.110] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 08:54:42.110] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 08:54:42.110] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 08:54:42.110] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 08:54:42.868] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 08:54:42.878] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 08:54:42.878] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 08:54:42.878] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 08:54:43.952] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 08:54:43.952] [puff::index::jointLog] [info] writing index components
[2022-05-27 08:54:44.007] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 09:07:03.713] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 09:07:04.173] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 09:07:04.173] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 09:07:04.223] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 09:07:04.353] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 09:07:13.840] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 09:07:13.840] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 09:07:13.863] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 09:07:13.864] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 09:07:13.885] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 09:07:13.885] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 09:07:13.887] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 09:07:13.887] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 09:07:13.891] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 09:07:13.904] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 09:07:13.904] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 09:07:13.912] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 09:07:13.989] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 09:07:13.989] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 09:07:13.989] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 09:07:13.989] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 09:07:13.989] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 09:07:14.780] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 09:07:14.790] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 09:07:14.790] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 09:07:14.790] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 09:07:15.859] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 09:07:15.859] [puff::index::jointLog] [info] writing index components
[2022-05-27 09:07:15.911] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 09:12:29.886] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 09:12:30.363] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 09:12:30.363] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 09:12:30.413] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 09:12:30.542] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 09:12:40.065] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 09:12:40.065] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 09:12:40.088] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 09:12:40.089] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 09:12:40.109] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 09:12:40.109] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 09:12:40.111] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 09:12:40.111] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 09:12:40.114] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 09:12:40.128] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 09:12:40.128] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 09:12:40.136] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 09:12:40.210] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 09:12:40.210] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 09:12:40.210] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 09:12:40.210] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 09:12:40.210] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 09:12:40.972] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 09:12:40.981] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 09:12:40.981] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 09:12:40.981] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 09:12:42.034] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 09:12:42.034] [puff::index::jointLog] [info] writing index components
[2022-05-27 09:12:42.085] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 09:15:12.965] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 09:15:13.458] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 09:15:13.458] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 09:15:13.509] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 09:15:13.639] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 09:15:23.049] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 09:15:23.049] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 09:15:23.072] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 09:15:23.072] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 09:15:23.093] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 09:15:23.093] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 09:15:23.096] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 09:15:23.096] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 09:15:23.099] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 09:15:23.112] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 09:15:23.112] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 09:15:23.120] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 09:15:23.195] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 09:15:23.195] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 09:15:23.195] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 09:15:23.195] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 09:15:23.195] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 09:15:23.971] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 09:15:23.982] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 09:15:23.982] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 09:15:23.982] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 09:15:25.032] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 09:15:25.032] [puff::index::jointLog] [info] writing index components
[2022-05-27 09:15:25.085] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 09:39:11.267] [puff::index::jointLog] [info] Running fixFasta
[2022-05-27 09:39:11.726] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 09:39:11.726] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
[2022-05-27 09:39:11.774] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 09:39:11.902] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
[2022-05-27 09:39:21.428] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 09:39:21.428] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
[2022-05-27 09:39:21.451] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 09:39:21.452] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 09:39:21.472] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 09:39:21.472] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 09:39:21.475] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 09:39:21.475] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 09:39:21.478] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 09:39:21.491] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 09:39:21.491] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 09:39:21.499] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] num keys = 12083744
[2022-05-27 09:39:22.357] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 09:39:22.368] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 09:39:22.368] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 09:39:22.368] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 09:39:23.395] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 09:39:23.395] [puff::index::jointLog] [info] writing index components
[2022-05-27 09:39:23.445] [puff::index::jointLog] [info] finished writing dense pufferfish index