Minimal example for mccortex threading bug

input.fasta

>0
CGTT
>1
CGTA

out.ctp.gz.log

[08 Oct 2018 17:14:42-cad][cmd] /usr/local/bin/mccortex31 thread -1 input.fasta -o out.ctp.gz out.ctx
[08 Oct 2018 17:14:42-cad][cwd] /Users/winni/tmp
[08 Oct 2018 17:14:42-cad][version] mccortex=v0.0.3-610-g400c0e3 zlib=1.2.11 htslib=1.8-17-g699ed53 ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31
[08 Oct 2018 17:14:42-cad] Reading graph: out.ctx
[08 Oct 2018 17:14:42-cad][task] input: input.fasta
[08 Oct 2018 17:14:42-cad]  FASTQ offset: auto-detect, threshold: off; cut homopolymers: off
[08 Oct 2018 17:14:42-cad]  one-way gap traversal [no edge check]
[08 Oct 2018 17:14:42-cad][memory] 140 bits per kmer
[08 Oct 2018 17:14:42-cad][memory] graph: 19.5KB
[08 Oct 2018 17:14:42-cad][memory] paths hash: 155.8MB
[08 Oct 2018 17:14:42-cad][memory] paths store: 356.2MB
[08 Oct 2018 17:14:42-cad][memory] total: 512MB of 16GB RAM
[08 Oct 2018 17:14:42-cad] Creating paths file: out.ctp.gz
[08 Oct 2018 17:14:42-cad][hasht] Allocating table with 1,024 entries, using 10KB
[08 Oct 2018 17:14:42-cad][hasht]  number of buckets: 1,024, bucket size: 1
[08 Oct 2018 17:14:42-cad][graph] kmer-size: 3; colours: 1; capacity: 1,024
[08 Oct 2018 17:14:42-cad][GPathSet] Allocating for 11,670,416 paths, 11.1MB colset, 133.6MB seq => 356.2MB total
[08 Oct 2018 17:14:42-cad][GPathHash] Allocating table with 16,777,216 entries, using 160.1MB
[08 Oct 2018 17:14:42-cad][GPathHash]  number of buckets: 524,288, bucket size: 32
[08 Oct 2018 17:14:42-cad] Not using new paths as they are added (safe)
[08 Oct 2018 17:14:42-cad][FileFilter] Reading file out.ctx [1 src colour]
[08 Oct 2018 17:14:42-cad][GReader] 3 kmers, 125B filesize
[08 Oct 2018 17:14:42-cad][GReader] Loaded 3 / 3 (100.00%) of kmers parsed
[08 Oct 2018 17:14:42-cad][hasht] buckets: 1,024 [2^10]; bucket size: 1; 
[08 Oct 2018 17:14:42-cad][hasht] memory: 10KB; filled: 3 / 1,024 (0.29%)
[08 Oct 2018 17:14:42-cad][GPathStore] Creating separate read/write GraphPath linked lists
[08 Oct 2018 17:14:42-cad][asyncio] Inputs: 1; Threads: 2
[08 Oct 2018 17:14:42-cad][seq] Parsing sequence file input.fasta
[08 Oct 2018 17:14:42-cad][seq] Loaded 2 reads and 0 reads pairs (file: input.fasta)
[08 Oct 2018 17:14:42-cad][GPathHash] Paths: 0 / 16,777,216 occupancy [0.00%] 0B / 160MB [0.00]
[08 Oct 2018 17:14:42-cad][GPathSet] Paths: 0 / 11,670,416 [0.00%], seqs: 0B / 144.7MB [0.00%] (0 / 151715424)
[08 Oct 2018 17:14:42-cad][GPathStore] kmers-with-paths: 0, num paths: 0, path-bytes: 0B
[08 Oct 2018 17:14:42-cad][CorrectAln] No gap attempts
[08 Oct 2018 17:14:42-cad][SeqStats] single reads: 2; read pairs: 0; total: 2
[08 Oct 2018 17:14:42-cad][SeqStats] Input coverage: 1.33X (4 / 3) reconstructed: 1.33X (4 / 3)
[08 Oct 2018 17:14:42-cad][SeqStats]  mean reconstructed contig length: 2 (kmers)
[08 Oct 2018 17:14:42-cad] Saving 0 paths to: out.ctp.gz
[08 Oct 2018 17:14:42-cad]  using 2 threads
[08 Oct 2018 17:14:42-cad][GPathSave] Graph paths saved to out.ctp.gz
[08 Oct 2018 17:14:42-cad][GPathStore] Merging read/write GraphPath linked lists
[08 Oct 2018 17:14:42-cad][memory] We made 33 allocs
[08 Oct 2018 17:14:42-cad] Done.
[08 Oct 2018 17:14:42-cad][time] 0.00 seconds

out.ctx.log

[08 Oct 2018 17:14:30-ZEg][cmd] /usr/local/bin/mccortex31 build -k 3 -s 0 -1 input.fasta out.ctx
[08 Oct 2018 17:14:30-ZEg][cwd] /Users/winni/tmp
[08 Oct 2018 17:14:30-ZEg][version] mccortex=v0.0.3-610-g400c0e3 zlib=1.2.11 htslib=1.8-17-g699ed53 ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31
[08 Oct 2018 17:14:30-ZEg] Saving graph to: out.ctx
[08 Oct 2018 17:14:30-ZEg][sample] 0: 0
[08 Oct 2018 17:14:30-ZEg][task] input.fasta; FASTQ offset: auto-detect, threshold: off; cut homopolymers: off; remove PCR duplicates: no; colour: 0
[08 Oct 2018 17:14:30-ZEg][memory] 104 bits per kmer
[08 Oct 2018 17:14:30-ZEg][memory] graph: 15KB
[08 Oct 2018 17:14:30-ZEg][memory] total: 15KB of 16GB RAM
[08 Oct 2018 17:14:30-ZEg] Writing 1 colour graph to out.ctx
[08 Oct 2018 17:14:30-ZEg][hasht] Allocating table with 1,024 entries, using 10KB
[08 Oct 2018 17:14:30-ZEg][hasht]  number of buckets: 1,024, bucket size: 1
[08 Oct 2018 17:14:30-ZEg][graph] kmer-size: 3; colours: 1; capacity: 1,024
[08 Oct 2018 17:14:30-ZEg][hasht] buckets: 1,024 [2^10]; bucket size: 1; 
[08 Oct 2018 17:14:30-ZEg][hasht] memory: 10KB; filled: 0 / 1,024 (0.00%)
[08 Oct 2018 17:14:30-ZEg][asyncio] Inputs: 1; Threads: 2
[08 Oct 2018 17:14:30-ZEg][seq] Parsing sequence file input.fasta
[08 Oct 2018 17:14:30-ZEg][seq] Loaded 2 reads and 0 reads pairs (file: input.fasta)
[08 Oct 2018 17:14:30-ZEg][hasht] buckets: 1,024 [2^10]; bucket size: 1; 
[08 Oct 2018 17:14:30-ZEg][hasht] memory: 10KB; filled: 3 / 1,024 (0.29%)
[08 Oct 2018 17:14:30-ZEg][hasht]  collisions  0: 3
[08 Oct 2018 17:14:30-ZEg][task] input: input.fasta colour: 0
[08 Oct 2018 17:14:30-ZEg]  SE reads: 2  PE reads: 0
[08 Oct 2018 17:14:30-ZEg]  good reads: 2  bad reads: 0
[08 Oct 2018 17:14:30-ZEg]  dup SE reads: 0  dup PE pairs: 0
[08 Oct 2018 17:14:30-ZEg]  bases read: 8  bases loaded: 8
[08 Oct 2018 17:14:30-ZEg]  num contigs: 2  num kmers: 4 novel kmers: 3
[08 Oct 2018 17:14:30-ZEg] Dumping graph...
[08 Oct 2018 17:14:30-ZEg][graphwriter] Saving file to: out.ctx
[08 Oct 2018 17:14:30-ZEg][FileFilter] Writing graph  [1 src colour]
[08 Oct 2018 17:14:30-ZEg][graphwriter] Dumped 3 kmers in 1 colour into: out.ctx (ver: 6)
[08 Oct 2018 17:14:30-ZEg][memory] We made 21 allocs
[08 Oct 2018 17:14:30-ZEg] Done.
[08 Oct 2018 17:14:30-ZEg][time] 0.00 seconds

script.sh

mccortex 3 build -k 3 -s 0 -1 input.fasta out.ctx 2> out.ctx.log
mccortex 3 thread -1 input.fasta -o out.ctp.gz out.ctx 2> out.ctp.gz.log