Non-reproducible error when computing Eulertigs with GGCAT2

[sebschmi]

I computed Eulertigs with GGCAT2 on a pangenome of 3681 E. coli genomes. I used ggcat as follows:

ggcat build -m 128 -k 27 -j 128 -s 1 --fast-eulertigs references.fa -o eulertigs.fa -t workdir

When I compared the resulting k-mer set against unitigs computed by GGCAT 1, my checking tool discovered the following differing k-mers:

10:06:29 [INFO] Reading first input file
10:06:56 [INFO] Sorting kmers in first input file
10:07:00 [INFO] Removing duplicates from first input file
10:07:00 [DEBUG] (1) verify_same_kmer_content: Duplicate kmers: 0/161002583 (0%)
10:07:00 [INFO] Reading second input file
10:07:25 [INFO] Sorting kmers in second input file
10:07:30 [INFO] Removing duplicates from second input file
10:07:30 [DEBUG] (1) verify_same_kmer_content: Duplicate kmers: 0/161002583 (0%)
10:07:30 [INFO] Comparing kmer content
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AAAATAGTGAAATTGCAGACAGCGTGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AAAATCAGATGAAATTGCAAATAAAGG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AAAATCAGATGAAATTGCAGACAGCGT
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AAAGTGAAATTGCAGACAGCGTGACAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AAATAAAGGCGCTGGATGTCGAGCAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AAATAGTGAAATTGCAGACAGCGTGAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AAATCAGATGAAATTGCAAATAAAGGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AAATCAGATGAAATTGCAGACAGCGTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AAATTGCAAATAAAGGCGCTGGATGTC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AAATTGCAGACAGCGTGACAAAATAGT
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AAGTGAAATTGCAGACAGCGTGACAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AATAAAGGCGCTGGATGTCGAGCAAAT
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AATAGTGAAATTGCAGACAGCGTGACA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AATCAGATGAAATTGCAAATAAAGGCG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AATCAGATGAAATTGCAGACAGCGTGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AATTGCAAATAAAGGCGCTGGATGTCG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AATTGCAGACAGCGTGACAAAATAGTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AATTTCACTATTTTGTCACGCTGTCTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AATTTCACTTTGTCACGCTGTCAGATG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AATTTCATCTAAAGGCGCTGGATGTCG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AATTTCATCTGACAGCGTGACAAAGTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AATTTGCTCGACATCCAGCGCCTTTAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AATTTGCTCGACATCCAGCGCCTTTAT
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ACAAAATAGTGAAATTGCAGACAGCGT
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACAAAATCAGATGAAATTGCAAATAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ACAAAATCAGATGAAATTGCAGACAGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACAAAGTGAAATTGCAGACAGCGTGAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ACAGCGTGACAAAATAGTGAAATTGCA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACAGCGTGACAAAGTGAAATTGCAGAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ACATCCAGCGCCTTTAGATGAAATTGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACATCCAGCGCCTTTATTTGCAATTTC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACGCTGTCAGATGAAATTGCAGACAGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACGCTGTCTGCAATTTCACTTTGTCAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ACGCTGTCTGCAATTTCATCTAAAGGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACGCTGTCTGCAATTTCATCTGACAGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ACTTTGTCACGCTGTCAGATGAAATTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AGACAGCGTGACAAAATAGTGAAATTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AGATGAAATTGCAAATAAAGGCGCTGG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AGATGAAATTGCAGACAGCGTGACAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AGCGCCTTTAGATGAAATTGCAGACAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AGCGCCTTTATTTGCAATTTCATCTGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: AGCGTGACAAAATAGTGAAATTGCAGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: AGCGTGACAAAGTGAAATTGCAGACAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATAGTGAAATTGCAGACAGCGTGACAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ATCAGATGAAATTGCAAATAAAGGCGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATCAGATGAAATTGCAGACAGCGTGAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATCCAGCGCCTTTAGATGAAATTGCAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ATCCAGCGCCTTTATTTGCAATTTCAT
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATCTAAAGGCGCTGGATGTCGAGCAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ATCTGACAGCGTGACAAAGTGAAATTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATGAAATTGCAGACAGCGTGACAAAAT
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ATTGCAAATAAAGGCGCTGGATGTCGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATTGCAGACAGCGTGACAAAATAGTGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATTTCACTATTTTGTCACGCTGTCTGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ATTTCACTTTGTCACGCTGTCAGATGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATTTCATCTAAAGGCGCTGGATGTCGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ATTTCATCTGACAGCGTGACAAAGTGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: ATTTGCAATTTCATCTGATTTTGTCAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: ATTTGCTCGACATCCAGCGCCTTTAGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CAAAATAGTGAAATTGCAGACAGCGTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CAAAATCAGATGAAATTGCAAATAAAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CAAAATCAGATGAAATTGCAGACAGCG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CAAAGTGAAATTGCAGACAGCGTGACA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CAAATAAAGGCGCTGGATGTCGAGCAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CAATTTCATCTAAAGGCGCTGGATGTC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CACGCTGTCAGATGAAATTGCAGACAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CACGCTGTCTGCAATTTCACTTTGTCA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CACGCTGTCTGCAATTTCATCTAAAGG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CACGCTGTCTGCAATTTCATCTGACAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CAGATGAAATTGCAAATAAAGGCGCTG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CAGCGCCTTTAGATGAAATTGCAGACA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CAGCGTGACAAAATAGTGAAATTGCAG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CAGCGTGACAAAGTGAAATTGCAGACA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CATCCAGCGCCTTTAGATGAAATTGCA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CATCCAGCGCCTTTATTTGCAATTTCA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CATCTAAAGGCGCTGGATGTCGAGCAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CCAGCGCCTTTAGATGAAATTGCAGAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CGCCTTTAGATGAAATTGCAGACAGCG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CGCTGTCAGATGAAATTGCAGACAGCG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CGCTGTCTGCAATTTCACTATTTTGTC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CGCTGTCTGCAATTTCACTTTGTCACG
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CGTGACAAAATAGTGAAATTGCAGACA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CGTGACAAAATCAGATGAAATTGCAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CGTGACAAAATCAGATGAAATTGCAGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CTATTTTGTCACGCTGTCTGCAATTTC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CTCGACATCCAGCGCCTTTAGATGAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CTCGACATCCAGCGCCTTTATTTGCAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CTGACAGCGTGACAAAGTGAAATTGCA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CTGCAATTTCACTTTGTCACGCTGTCA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CTGCAATTTCATCTGACAGCGTGACAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CTGCAATTTCATCTGATTTTGTCACGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CTGTCTGCAATTTCACTATTTTGTCAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CTGTCTGCAATTTCATCTGATTTTGTC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: CTTTAGATGAAATTGCAGACAGCGTGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: CTTTGTCACGCTGTCAGATGAAATTGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GACAAAATCAGATGAAATTGCAAATAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GACAAAGTGAAATTGCAGACAGCGTGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GACAGCGTGACAAAATAGTGAAATTGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GACAGCGTGACAAAGTGAAATTGCAGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GATGAAATTGCAAATAAAGGCGCTGGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GATGAAATTGCAGACAGCGTGACAAAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GCAAATAAAGGCGCTGGATGTCGAGCA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GCAATTTCACTTTGTCACGCTGTCAGA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GCGCCTTTAGATGAAATTGCAGACAGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GCGTGACAAAATAGTGAAATTGCAGAC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GCGTGACAAAATCAGATGAAATTGCAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GCGTGACAAAGTGAAATTGCAGACAGC
10:07:30 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GCTCGACATCCAGCGCCTTTAGATGAA
10:07:30 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GCTCGACATCCAGCGCCTTTATTTGCA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GCTGTCTGCAATTTCACTATTTTGTCA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GTCACGCTGTCAGATGAAATTGCAGAC
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GTCACGCTGTCTGCAATTTCATCTAAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: GTCACGCTGTCTGCAATTTCATCTGAC
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: GTCTGCAATTTCATCTGATTTTGTCAC
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TAGATGAAATTGCAGACAGCGTGACAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TAGTGAAATTGCAGACAGCGTGACAAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: TATTTGCAATTTCATCTGATTTTGTCA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TATTTTGTCACGCTGTCTGCAATTTCA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: TCACGCTGTCAGATGAAATTGCAGACA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: TCACGCTGTCTGCAATTTCATCTGACA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TCATCTAAAGGCGCTGGATGTCGAGCA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TCCAGCGCCTTTAGATGAAATTGCAGA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: TCTGCAATTTCATCTGACAGCGTGACA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TGACAAAATCAGATGAAATTGCAGACA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: TGCAATTTCATCTGACAGCGTGACAAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TGCAGACAGCGTGACAAAATAGTGAAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TGTCACGCTGTCTGCAATTTCATCTAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Unitigs contain kmer that is missing in test tigs: TTCACTATTTTGTCACGCTGTCTGCAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: TTCACTTTGTCACGCTGTCAGATGAAA
10:07:31 [DEBUG] (1) verify_same_kmer_content: Test tigs contains kmer that is missing in unitigs: TTCATCTGACAGCGTGACAAAGTGAAA
10:07:31 [INFO] Test tigs miss 65 kmers that are present in unitigs
10:07:31 [INFO] Test tigs contain 65 kmers that are not present in unitigs
ground_truth_size:   400956037
test_size: 234742951
ground_truth_str_cnt:   9228979
test_str_cnt: 2836168
compression_rate: 0.5854580785374233
str_cnt_rate: 0.3073111337668013
unique_kmer_count: 161002583
10:07:31 [ERROR] Test tigs both miss kmers and contain kmers that are not present in unitigs

After running GGCAT2 again with the above arguments, the output was correct. And I am not able to reproduce the error again.

Note that the number of k-mers is the same, just some of them have changed into a different one.

I am using GGCAT2 at commit 08ccdb6.