Sebastien-Raguideau
commented
4 years ago issue not replicable. Due to bad install/previous install/previous version/....
Closed KimSummers closed 4 years ago
Sebastien-Raguideau
commented
4 years ago issue not replicable. Due to bad install/previous install/previous version/....
Got error unitig-coverage: /home/ubuntu/Programs/STRONG/SPAdes/assembler/src/projects/unitig_coverage/main.cpp:36: io::ReadStreamList single_easy_readers_for_libs(DataSet&, const std::vector&, bool, bool, bool, io::OffsetType): Assertion `!libs.empty()' failed.
in the simplified.mult_prof.log file when running STRONG on a clean install vm.
Contents of log are:
0:00:00.000 4M / 5M INFO General (main.cpp : 118) Starting Computing unitig coverage profiles across a list of samples, built from N/A, git revision N/A 0:00:00.003 4M / 5M INFO General (main.cpp : 127) K-mer length set to 77 0:00:00.003 4M / 5M INFO General (main.cpp : 132) # of threads to use: 8 0:00:00.005 4M / 5M INFO General (main.cpp : 53) Loading de Bruijn graph from assembly/high_res/simplified.gfa 0:00:00.744 100M / 101M INFO General (utils.hpp : 35) GFA segments: 124057, links: 331044 0:00:01.756 148M / 183M INFO General (utils.hpp : 40) Graph loaded. Total vertices: 496228 Total edges: 248114 0:00:01.756 148M / 183M INFO General (graph_pack.hpp : 105) Index refill 0:00:01.756 148M / 183M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:01.758 148M / 183M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while. 0:00:01.759 148M / 183M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:01.759 148M / 183M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 7.15828e+08 Gb 0:00:01.759 148M / 183M INFO General (kmer_splitters.hpp : 97) Using cell size of 174762 0:00:03.756 6G / 6G INFO General (edge_index_builders.hpp : 77) Processed 248114 edges 0:00:03.757 6G / 6G INFO General (edge_index_builders.hpp : 82) Used 248114 sequences. 0:00:03.839 266M / 1003M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.570 264M / 1003M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 34755666 kmers in total. 0:00:04.570 264M / 1003M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.675 264M / 1003M INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:07.033 233M / 1003M INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:11.688 233M / 1003M INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 16124448 bytes occupied (3.7115 bits per kmer). 0:00:12.427 875M / 1003M INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:16.831 799M / 1003M INFO General (edge_index.hpp : 92) Index refilled 0:00:16.832 799M / 1003M INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 0 kmers to process 0:00:16.833 799M / 1003M INFO General (graph_pack.hpp : 115) Normalizing done unitig-coverage: /home/ubuntu/Programs/STRONG/SPAdes/assembler/src/projects/unitig_coverage/main.cpp:36: io::ReadStreamList single_easy_readers_for_libs(DataSet&, const std::vector&, bool, bool, bool, io::OffsetType): Assertion `!libs.empty()' failed.