Cuttlefish3 segfaults randomly on a standard E.coli pangenome #52
Description
Dataset:
3681 E. Coli genomes used in e.g. the Eulertigs paper. One genome has since been deleted from NCBI and was hence not included.
Command:
bin/cuttlefish build -m 128 -s references.fa -k 27 -t 128 --path-cover -o unitigs -w workdir --ref -c 1
Additional Info:
The same command works with -k 63, or without --path-cover.
Log:
Constructing the compacted reference de Bruijn graph for k = 27.
Edge frequency cutoff: 1.
Partitioned 18333 MB of uncompressed data.
Number of processed chunks: 2413.
Total size of chunks: 19224055383.
Number of records: 745406.
Number of super (k - 1)-mers: 2359174334.
Total length of the weak super k-mers: 82590357521.
Total length of the super (k - 1)-mers: 77873499665.
Total work in parse: 24.7938s.
Total work in processing records: 492.486s.
Max work in processing records: 492.486s.
Total atlas size in bytes: 47183486680.
Sequence splitting into subgraphs completed. Time taken: 529.71 seconds.
Solved 16384 subgraphs.16064 subgraphs.16067 subgraphs.16067 subgraphs.
Total work in graph construction: 1383.89 (s).
Total work in graph contraction: 120.739 (s).
Total work in bucket removal: 94.8811 (s).
Maximum k-mer count in bucket: 5569711.
Minimum k-mer count in bucket: 412034.
Sum graph size: 181111067.
Largest graph size: 100994.
Smallest graph size: 5275.
Sum label size: 940099714.
Bytes in super k-mer buckets: 47183486680.
Bytes in compressed super k-mer buckets: 22227158678.
lm-tig count: 29192097.
Trivial maximal unitig count: 3441242.
Trivial ICC count: 0.
Subgraphs construction and contraction completed. Time taken: 6.35336 seconds.
Edge-matrix size: 25750855
Phantom edge upper-bound: 5875
Expecting at most 5648246 more non-DCC maximal unitigs
Hash table capacity during contraction: 1048576.
Part: 10
Formed 5648254 meta-vertices.
Found 8 ICCs.
Found 5875 phantoms.
Map clearing time: 0.150711.
Non-diagonal edges contraction time: 1.73894.
Diagonal-chain computation time: 0.439419.
Diagonal-chain contraction time: 0.343218.
Filtering in false-phantom edges time: 0.138168.
Discontinuity-graph contraction completed. Time taken: 3.52024 seconds.
Hash table capacity during expansion: 1048576.
Part: 64
Map clearing time: 0.191931.
Path-info load time: 0.866394.
Non-diagonal blocks expansion time: 1.21174.
Diagonal block expansion time: 0.199794.
Special case time: 1.73619.
Deletion time: 0.117828.
Expansion of contracted graph completed. Time taken: 4.8203 seconds.
Sum edge-bucket size: 25756730
Maximum edge-bucket size: 34894
Found 25756730 edges.
Time taken in mapping: 1.24098s.
Maximum maximal unitig bucket size: 33801
Maximum label length in mtig-buckets: 1124388
Peak-RAM before collation: 36.1891
Command terminated by signal 11