GraphUnzip crashed - Githubissues

I tried running GraphUnzip on a SPAdes Illumina assembly of a ca. 250 Mb genome, after aligning 156 000 Nanopore reads > 10 kb in length on the GFA using SPAligner (command: spaligner spaligner_config.yaml -d nanopore -s ONT_10kbmin.fastq -g SPADES_nanopore_assembly_graph_with_scaffolds.gfa -k 77 -t 14 -o spaligner. Alignment went well, with > 99.9% of reads mapping on the graph. However, GraphUnzip crashed afterward (command: graphunzip.py -g SPADES_assembly_graph_with_scaffolds.gfa -l spaligner/alignment.tsv -o SPADES_assembly_graph_with_scaffolds_GraphUnzip.gfa -f SPADES_assembly_graph_with_scaffolds_GraphUnzip.fasta unzip). Here is the log:

Loading the GFA file Loading contigs Loading links Everything loaded, moving on to untangling the graph Reading the gpa file... Finished going through the gpa file. Inventoried 1000 long reads over 73428 Inventoried 2000 long reads over 73428 Inventoried 3000 long reads over 73428 Inventoried 4000 long reads over 73428 Inventoried 5000 long reads over 73428 Inventoried 6000 long reads over 73428 Inventoried 7000 long reads over 73428 Inventoried 8000 long reads over 73428 Inventoried 9000 long reads over 73428 Inventoried 10000 long reads over 73428 Inventoried 11000 long reads over 73428 Inventoried 12000 long reads over 73428 Inventoried 13000 long reads over 73428 Inventoried 14000 long reads over 73428 Inventoried 15000 long reads over 73428 Inventoried 16000 long reads over 73428 Inventoried 17000 long reads over 73428 Inventoried 18000 long reads over 73428 Inventoried 19000 long reads over 73428 Inventoried 20000 long reads over 73428 Inventoried 21000 long reads over 73428 Inventoried 22000 long reads over 73428 Inventoried 23000 long reads over 73428 Inventoried 24000 long reads over 73428 Inventoried 25000 long reads over 73428 Inventoried 26000 long reads over 73428 Inventoried 27000 long reads over 73428 Inventoried 28000 long reads over 73428 Inventoried 29000 long reads over 73428 Inventoried 30000 long reads over 73428 Inventoried 31000 long reads over 73428 Inventoried 32000 long reads over 73428 Inventoried 33000 long reads over 73428 Inventoried 34000 long reads over 73428 Inventoried 35000 long reads over 73428 Inventoried 36000 long reads over 73428 Inventoried 37000 long reads over 73428 Inventoried 38000 long reads over 73428 Inventoried 39000 long reads over 73428 Inventoried 40000 long reads over 73428 Inventoried 41000 long reads over 73428 Inventoried 42000 long reads over 73428 Inventoried 43000 long reads over 73428 Inventoried 44000 long reads over 73428 Inventoried 45000 long reads over 73428 Inventoried 46000 long reads over 73428 Inventoried 47000 long reads over 73428 Inventoried 48000 long reads over 73428 Inventoried 49000 long reads over 73428 Inventoried 50000 long reads over 73428 Inventoried 51000 long reads over 73428 Inventoried 52000 long reads over 73428 Inventoried 53000 long reads over 73428 Inventoried 54000 long reads over 73428 Inventoried 55000 long reads over 73428 Inventoried 56000 long reads over 73428 Inventoried 57000 long reads over 73428 Inventoried 58000 long reads over 73428 Inventoried 59000 long reads over 73428 Inventoried 60000 long reads over 73428 Inventoried 61000 long reads over 73428 Inventoried 62000 long reads over 73428 Inventoried 63000 long reads over 73428 Inventoried 64000 long reads over 73428 Inventoried 65000 long reads over 73428 Inventoried 66000 long reads over 73428 Inventoried 67000 long reads over 73428 Inventoried 68000 long reads over 73428 Inventoried 69000 long reads over 73428 Inventoried 70000 long reads over 73428 Inventoried 71000 long reads over 73428 Inventoried 72000 long reads over 73428 Inventoried 73000 long reads over 73428 Building consensus bridges from all the long reads consensused 0 bridges out of 51462 consensused 100 bridges out of 51462 consensused 200 bridges out of 51462 consensused 300 bridges out of 51462 consensused 400 bridges out of 51462 consensused 500 bridges out of 51462 consensused 600 bridges out of 51462 consensused 700 bridges out of 51462 consensused 800 bridges out of 51462 consensused 900 bridges out of 51462 consensused 1000 bridges out of 51462 consensused 1100 bridges out of 51462 consensused 1200 bridges out of 51462 consensused 1300 bridges out of 51462 consensused 1400 bridges out of 51462 consensused 1500 bridges out of 51462 consensused 1600 bridges out of 51462 consensused 1700 bridges out of 51462 consensused 1800 bridges out of 51462 consensused 1900 bridges out of 51462 consensused 2000 bridges out of 51462 consensused 2100 bridges out of 51462 consensused 2200 bridges out of 51462 consensused 2300 bridges out of 51462 consensused 2400 bridges out of 51462 consensused 2500 bridges out of 51462 consensused 2600 bridges out of 51462 consensused 2700 bridges out of 51462 consensused 2800 bridges out of 51462 consensused 2900 bridges out of 51462 consensused 3000 bridges out of 51462 consensused 3100 bridges out of 51462 consensused 3200 bridges out of 51462 consensused 3300 bridges out of 51462 consensused 3400 bridges out of 51462 consensused 3500 bridges out of 51462 consensused 3600 bridges out of 51462 consensused 3700 bridges out of 51462 consensused 3800 bridges out of 51462 consensused 3900 bridges out of 51462 consensused 4000 bridges out of 51462 consensused 4100 bridges out of 51462 consensused 4200 bridges out of 51462 consensused 4300 bridges out of 51462 consensused 4400 bridges out of 51462 consensused 4500 bridges out of 51462 consensused 4600 bridges out of 51462 consensused 4700 bridges out of 51462 consensused 4800 bridges out of 51462 consensused 4900 bridges out of 51462 consensused 5000 bridges out of 51462 consensused 5100 bridges out of 51462 consensused 5200 bridges out of 51462 consensused 5300 bridges out of 51462 consensused 5400 bridges out of 51462 consensused 5500 bridges out of 51462 consensused 5600 bridges out of 51462 consensused 5700 bridges out of 51462 consensused 5800 bridges out of 51462 consensused 5900 bridges out of 51462 consensused 6000 bridges out of 51462 consensused 6100 bridges out of 51462 consensused 6200 bridges out of 51462 consensused 6300 bridges out of 51462 consensused 6400 bridges out of 51462 consensused 6500 bridges out of 51462 consensused 6600 bridges out of 51462 consensused 6700 bridges out of 51462 consensused 6800 bridges out of 51462 consensused 6900 bridges out of 51462 consensused 7000 bridges out of 51462 consensused 7100 bridges out of 51462 consensused 7200 bridges out of 51462 consensused 7300 bridges out of 51462 consensused 7400 bridges out of 51462 consensused 7500 bridges out of 51462 consensused 7600 bridges out of 51462 consensused 7700 bridges out of 51462 consensused 7800 bridges out of 51462 consensused 7900 bridges out of 51462 consensused 8000 bridges out of 51462 consensused 8100 bridges out of 51462 consensused 8200 bridges out of 51462 consensused 8300 bridges out of 51462 consensused 8400 bridges out of 51462 consensused 8500 bridges out of 51462 consensused 8600 bridges out of 51462 consensused 8700 bridges out of 51462 consensused 8800 bridges out of 51462 consensused 8900 bridges out of 51462 consensused 9000 bridges out of 51462 consensused 9100 bridges out of 51462 consensused 9200 bridges out of 51462 consensused 9300 bridges out of 51462 consensused 9400 bridges out of 51462 consensused 9500 bridges out of 51462 consensused 9600 bridges out of 51462 consensused 9700 bridges out of 51462 consensused 9800 bridges out of 51462 consensused 9900 bridges out of 51462 consensused 10000 bridges out of 51462 consensused 10100 bridges out of 51462 consensused 10200 bridges out of 51462 consensused 10300 bridges out of 51462 consensused 10400 bridges out of 51462 consensused 10500 bridges out of 51462 consensused 10600 bridges out of 51462 consensused 10700 bridges out of 51462 consensused 10800 bridges out of 51462 consensused 10900 bridges out of 51462 consensused 11000 bridges out of 51462 consensused 11100 bridges out of 51462 consensused 11200 bridges out of 51462 consensused 11300 bridges out of 51462 consensused 11400 bridges out of 51462 consensused 11500 bridges out of 51462 consensused 11600 bridges out of 51462 consensused 11700 bridges out of 51462 consensused 11800 bridges out of 51462 consensused 11900 bridges out of 51462 consensused 12000 bridges out of 51462 consensused 12100 bridges out of 51462 consensused 12200 bridges out of 51462 consensused 12300 bridges out of 51462 consensused 12400 bridges out of 51462 consensused 12500 bridges out of 51462 consensused 12600 bridges out of 51462 consensused 12700 bridges out of 51462 consensused 12800 bridges out of 51462 consensused 12900 bridges out of 51462 consensused 13000 bridges out of 51462 consensused 13100 bridges out of 51462 consensused 13200 bridges out of 51462 consensused 13300 bridges out of 51462 consensused 13400 bridges out of 51462 consensused 13500 bridges out of 51462 consensused 13600 bridges out of 51462 consensused 13700 bridges out of 51462 consensused 13800 bridges out of 51462 consensused 13900 bridges out of 51462 consensused 14000 bridges out of 51462 consensused 14100 bridges out of 51462 consensused 14200 bridges out of 51462 consensused 14300 bridges out of 51462 consensused 14400 bridges out of 51462 consensused 14500 bridges out of 51462 consensused 14600 bridges out of 51462 consensused 14700 bridges out of 51462 consensused 14800 bridges out of 51462 consensused 14900 bridges out of 51462 consensused 15000 bridges out of 51462 consensused 15100 bridges out of 51462 consensused 15200 bridges out of 51462 consensused 15300 bridges out of 51462 consensused 15400 bridges out of 51462 consensused 15500 bridges out of 51462 consensused 15600 bridges out of 51462 consensused 15700 bridges out of 51462 consensused 15800 bridges out of 51462 consensused 15900 bridges out of 51462 consensused 16000 bridges out of 51462 consensused 16100 bridges out of 51462 consensused 16200 bridges out of 51462 consensused 16300 bridges out of 51462 consensused 16400 bridges out of 51462 consensused 16500 bridges out of 51462 consensused 16600 bridges out of 51462 consensused 16700 bridges out of 51462 consensused 16800 bridges out of 51462 consensused 16900 bridges out of 51462 consensused 17000 bridges out of 51462 consensused 17100 bridges out of 51462 consensused 17200 bridges out of 51462 consensused 17300 bridges out of 51462 consensused 17400 bridges out of 51462 consensused 17500 bridges out of 51462 consensused 17600 bridges out of 51462 consensused 17700 bridges out of 51462 consensused 17800 bridges out of 51462 consensused 17900 bridges out of 51462 consensused 18000 bridges out of 51462 consensused 18100 bridges out of 51462 consensused 18200 bridges out of 51462 consensused 18300 bridges out of 51462 consensused 18400 bridges out of 51462 consensused 18500 bridges out of 51462 consensused 18600 bridges out of 51462 consensused 18700 bridges out of 51462 consensused 18800 bridges out of 51462 consensused 18900 bridges out of 51462 consensused 19000 bridges out of 51462 consensused 19100 bridges out of 51462 consensused 19200 bridges out of 51462 consensused 19300 bridges out of 51462 consensused 19400 bridges out of 51462 consensused 19500 bridges out of 51462 consensused 19600 bridges out of 51462 consensused 19700 bridges out of 51462 consensused 19800 bridges out of 51462 consensused 19900 bridges out of 51462 consensused 20000 bridges out of 51462 consensused 20100 bridges out of 51462 consensused 20200 bridges out of 51462 consensused 20300 bridges out of 51462 consensused 20400 bridges out of 51462 consensused 20500 bridges out of 51462 consensused 20600 bridges out of 51462 consensused 20700 bridges out of 51462 consensused 20800 bridges out of 51462 consensused 20900 bridges out of 51462 consensused 21000 bridges out of 51462 consensused 21100 bridges out of 51462 consensused 21200 bridges out of 51462 consensused 21300 bridges out of 51462 consensused 21400 bridges out of 51462 consensused 21500 bridges out of 51462 consensused 21600 bridges out of 51462 consensused 21700 bridges out of 51462 consensused 21800 bridges out of 51462 consensused 21900 bridges out of 51462 consensused 22000 bridges out of 51462 consensused 22100 bridges out of 51462 consensused 22200 bridges out of 51462 consensused 22300 bridges out of 51462 consensused 22400 bridges out of 51462 consensused 22500 bridges out of 51462 consensused 22600 bridges out of 51462 consensused 22700 bridges out of 51462 consensused 22800 bridges out of 51462 consensused 22900 bridges out of 51462 consensused 23000 bridges out of 51462 consensused 23100 bridges out of 51462 consensused 23200 bridges out of 51462 consensused 23300 bridges out of 51462 consensused 23400 bridges out of 51462 consensused 23500 bridges out of 51462 consensused 23600 bridges out of 51462 consensused 23700 bridges out of 51462 consensused 23800 bridges out of 51462 consensused 23900 bridges out of 51462 consensused 24000 bridges out of 51462 consensused 24100 bridges out of 51462 consensused 24200 bridges out of 51462 consensused 24300 bridges out of 51462 consensused 24400 bridges out of 51462 consensused 24500 bridges out of 51462 consensused 24600 bridges out of 51462 consensused 24700 bridges out of 51462 consensused 24800 bridges out of 51462 consensused 24900 bridges out of 51462 consensused 25000 bridges out of 51462 consensused 25100 bridges out of 51462 consensused 25200 bridges out of 51462 consensused 25300 bridges out of 51462 consensused 25400 bridges out of 51462 consensused 25500 bridges out of 51462 consensused 25600 bridges out of 51462 consensused 25700 bridges out of 51462 consensused 25800 bridges out of 51462 consensused 25900 bridges out of 51462 consensused 26000 bridges out of 51462 consensused 26100 bridges out of 51462 consensused 26200 bridges out of 51462 consensused 26300 bridges out of 51462 consensused 26400 bridges out of 51462 consensused 26500 bridges out of 51462 consensused 26600 bridges out of 51462 consensused 26700 bridges out of 51462 consensused 26800 bridges out of 51462 consensused 26900 bridges out of 51462 consensused 27000 bridges out of 51462 consensused 27100 bridges out of 51462 consensused 27200 bridges out of 51462 consensused 27300 bridges out of 51462 consensused 27400 bridges out of 51462 consensused 27500 bridges out of 51462 consensused 27600 bridges out of 51462 consensused 27700 bridges out of 51462 consensused 27800 bridges out of 51462 consensused 27900 bridges out of 51462 consensused 28000 bridges out of 51462 consensused 28100 bridges out of 51462 consensused 28200 bridges out of 51462 consensused 28300 bridges out of 51462 consensused 28400 bridges out of 51462 consensused 28500 bridges out of 51462 consensused 28600 bridges out of 51462 consensused 28700 bridges out of 51462 consensused 28800 bridges out of 51462 consensused 28900 bridges out of 51462 consensused 29000 bridges out of 51462 consensused 29100 bridges out of 51462 consensused 29200 bridges out of 51462 consensused 29300 bridges out of 51462 consensused 29400 bridges out of 51462 consensused 29500 bridges out of 51462 consensused 29600 bridges out of 51462 consensused 29700 bridges out of 51462 consensused 29800 bridges out of 51462 consensused 29900 bridges out of 51462 consensused 30000 bridges out of 51462 consensused 30100 bridges out of 51462 consensused 30200 bridges out of 51462 consensused 30300 bridges out of 51462 consensused 30400 bridges out of 51462 consensused 30500 bridges out of 51462 consensused 30600 bridges out of 51462 consensused 30700 bridges out of 51462 consensused 30800 bridges out of 51462 consensused 30900 bridges out of 51462 consensused 31000 bridges out of 51462 consensused 31100 bridges out of 51462 consensused 31200 bridges out of 51462 consensused 31300 bridges out of 51462 consensused 31400 bridges out of 51462 consensused 31500 bridges out of 51462 consensused 31600 bridges out of 51462 consensused 31700 bridges out of 51462 consensused 31800 bridges out of 51462 consensused 31900 bridges out of 51462 consensused 32000 bridges out of 51462 consensused 32100 bridges out of 51462 consensused 32200 bridges out of 51462 consensused 32300 bridges out of 51462 consensused 32400 bridges out of 51462 consensused 32500 bridges out of 51462 consensused 32600 bridges out of 51462 consensused 32700 bridges out of 51462 consensused 32800 bridges out of 51462 consensused 32900 bridges out of 51462 consensused 33000 bridges out of 51462 consensused 33100 bridges out of 51462 consensused 33200 bridges out of 51462 consensused 33300 bridges out of 51462 consensused 33400 bridges out of 51462 consensused 33500 bridges out of 51462 consensused 33600 bridges out of 51462 consensused 33700 bridges out of 51462 consensused 33800 bridges out of 51462 consensused 33900 bridges out of 51462 consensused 34000 bridges out of 51462 consensused 34100 bridges out of 51462 consensused 34200 bridges out of 51462 consensused 34300 bridges out of 51462 consensused 34400 bridges out of 51462 consensused 34500 bridges out of 51462 consensused 34600 bridges out of 51462 consensused 34700 bridges out of 51462 consensused 34800 bridges out of 51462 consensused 34900 bridges out of 51462 consensused 35000 bridges out of 51462 consensused 35100 bridges out of 51462 consensused 35200 bridges out of 51462 consensused 35300 bridges out of 51462 consensused 35400 bridges out of 51462 consensused 35500 bridges out of 51462 consensused 35600 bridges out of 51462 consensused 35700 bridges out of 51462 consensused 35800 bridges out of 51462 consensused 35900 bridges out of 51462 consensused 36000 bridges out of 51462 consensused 36100 bridges out of 51462 consensused 36200 bridges out of 51462 consensused 36300 bridges out of 51462 consensused 36400 bridges out of 51462 consensused 36500 bridges out of 51462 consensused 36600 bridges out of 51462 consensused 36700 bridges out of 51462 consensused 36800 bridges out of 51462 consensused 36900 bridges out of 51462 consensused 37000 bridges out of 51462 consensused 37100 bridges out of 51462 consensused 37200 bridges out of 51462 consensused 37300 bridges out of 51462 consensused 37400 bridges out of 51462 consensused 37500 bridges out of 51462 consensused 37600 bridges out of 51462 consensused 37700 bridges out of 51462 consensused 37800 bridges out of 51462 consensused 37900 bridges out of 51462 consensused 38000 bridges out of 51462 consensused 38100 bridges out of 51462 consensused 38200 bridges out of 51462 consensused 38300 bridges out of 51462 consensused 38400 bridges out of 51462 consensused 38500 bridges out of 51462 consensused 38600 bridges out of 51462 consensused 38700 bridges out of 51462 consensused 38800 bridges out of 51462 consensused 38900 bridges out of 51462 consensused 39000 bridges out of 51462 consensused 39100 bridges out of 51462 consensused 39200 bridges out of 51462 consensused 39300 bridges out of 51462 consensused 39400 bridges out of 51462 consensused 39500 bridges out of 51462 consensused 39600 bridges out of 51462 consensused 39700 bridges out of 51462 consensused 39800 bridges out of 51462 consensused 39900 bridges out of 51462 consensused 40000 bridges out of 51462 consensused 40100 bridges out of 51462 consensused 40200 bridges out of 51462 consensused 40300 bridges out of 51462 consensused 40400 bridges out of 51462 consensused 40500 bridges out of 51462 consensused 40600 bridges out of 51462 consensused 40700 bridges out of 51462 consensused 40800 bridges out of 51462 consensused 40900 bridges out of 51462 consensused 41000 bridges out of 51462 consensused 41100 bridges out of 51462 consensused 41200 bridges out of 51462 consensused 41300 bridges out of 51462 consensused 41400 bridges out of 51462 consensused 41500 bridges out of 51462 consensused 41600 bridges out of 51462 consensused 41700 bridges out of 51462 consensused 41800 bridges out of 51462 consensused 41900 bridges out of 51462 consensused 42000 bridges out of 51462 consensused 42100 bridges out of 51462 consensused 42200 bridges out of 51462 consensused 42300 bridges out of 51462 consensused 42400 bridges out of 51462 consensused 42500 bridges out of 51462 consensused 42600 bridges out of 51462 consensused 42700 bridges out of 51462 consensused 42800 bridges out of 51462 consensused 42900 bridges out of 51462 consensused 43000 bridges out of 51462 consensused 43100 bridges out of 51462 consensused 43200 bridges out of 51462 consensused 43300 bridges out of 51462 consensused 43400 bridges out of 51462 consensused 43500 bridges out of 51462 consensused 43600 bridges out of 51462 consensused 43700 bridges out of 51462 consensused 43800 bridges out of 51462 consensused 43900 bridges out of 51462 consensused 44000 bridges out of 51462 consensused 44100 bridges out of 51462 consensused 44200 bridges out of 51462 consensused 44300 bridges out of 51462 consensused 44400 bridges out of 51462 consensused 44500 bridges out of 51462 consensused 44600 bridges out of 51462 consensused 44700 bridges out of 51462 consensused 44800 bridges out of 51462 consensused 44900 bridges out of 51462 consensused 45000 bridges out of 51462 consensused 45100 bridges out of 51462 consensused 45200 bridges out of 51462 consensused 45300 bridges out of 51462 consensused 45400 bridges out of 51462 consensused 45500 bridges out of 51462 consensused 45600 bridges out of 51462 consensused 45700 bridges out of 51462 consensused 45800 bridges out of 51462 consensused 45900 bridges out of 51462 consensused 46000 bridges out of 51462 consensused 46100 bridges out of 51462 consensused 46200 bridges out of 51462 consensused 46300 bridges out of 51462 consensused 46400 bridges out of 51462 consensused 46500 bridges out of 51462 consensused 46600 bridges out of 51462 consensused 46700 bridges out of 51462 consensused 46800 bridges out of 51462 consensused 46900 bridges out of 51462 consensused 47000 bridges out of 51462 consensused 47100 bridges out of 51462 consensused 47200 bridges out of 51462 consensused 47300 bridges out of 51462 consensused 47400 bridges out of 51462 consensused 47500 bridges out of 51462 consensused 47600 bridges out of 51462 consensused 47700 bridges out of 51462 consensused 47800 bridges out of 51462 consensused 47900 bridges out of 51462 consensused 48000 bridges out of 51462 consensused 48100 bridges out of 51462 consensused 48200 bridges out of 51462 consensused 48300 bridges out of 51462 consensused 48400 bridges out of 51462 consensused 48500 bridges out of 51462 consensused 48600 bridges out of 51462 consensused 48700 bridges out of 51462 consensused 48800 bridges out of 51462 consensused 48900 bridges out of 51462 consensused 49000 bridges out of 51462 consensused 49100 bridges out of 51462 consensused 49200 bridges out of 51462 consensused 49300 bridges out of 51462 consensused 49400 bridges out of 51462 consensused 49500 bridges out of 51462 consensused 49600 bridges out of 51462 consensused 49700 bridges out of 51462 consensused 49800 bridges out of 51462 consensused 49900 bridges out of 51462 consensused 50000 bridges out of 51462 consensused 50100 bridges out of 51462 consensused 50200 bridges out of 51462 consensused 50300 bridges out of 51462 consensused 50400 bridges out of 51462 consensused 50500 bridges out of 51462 consensused 50600 bridges out of 51462 consensused 50700 bridges out of 51462 consensused 50800 bridges out of 51462 consensused 50900 bridges out of 51462 consensused 51000 bridges out of 51462 consensused 51100 bridges out of 51462 consensused 51200 bridges out of 51462 consensused 51300 bridges out of 51462 consensused 51400 bridges out of 51462 Done building consensus bridges Now we will determine through an iterative process what contigs of the assembly are present only once in the final genome Out of 51462 supposed single-copy contigs, 11975 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 39487 supposed single-copy contigs, 4719 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 34768 supposed single-copy contigs, 2333 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 32435 supposed single-copy contigs, 1244 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 31191 supposed single-copy contigs, 744 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 30447 supposed single-copy contigs, 412 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 30035 supposed single-copy contigs, 253 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29782 supposed single-copy contigs, 148 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29634 supposed single-copy contigs, 92 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29542 supposed single-copy contigs, 59 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29483 supposed single-copy contigs, 37 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29446 supposed single-copy contigs, 30 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29416 supposed single-copy contigs, 21 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29395 supposed single-copy contigs, 13 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29382 supposed single-copy contigs, 8 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29374 supposed single-copy contigs, 6 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29368 supposed single-copy contigs, 4 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29364 supposed single-copy contigs, 3 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29361 supposed single-copy contigs, 3 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29358 supposed single-copy contigs, 3 were not actually haploid. Recomputing until all the single-copy contigs are robust. Out of 29355 supposed single-copy contigs, 1 were not actually haploid. Recomputing until all the single-copy contigs are robust. Let's move on to actually untangling the graph Processed 0 contigs out of 102461 , while untangling with long reads Processed 1000 contigs out of 102461 , while untangling with long reads Processed 2000 contigs out of 102461 , while untangling with long reads Processed 3000 contigs out of 102461 , while untangling with long reads Processed 4000 contigs out of 102461 , while untangling with long reads Debug WARNING, ['271376', '16521597', '272120', '77390718', '7591698'] : looking for ['7591698'] 0 from ['77390718'] among [['7591698'], ['14360169']] [1, 1] 271376 <16521597>272120<77390718>7591698 Processed 5000 contigs out of 102461 , while untangling with long reads Processed 6000 contigs out of 102461 , while untangling with long reads Processed 7000 contigs out of 102461 , while untangling with long reads Processed 8000 contigs out of 102461 , while untangling with long reads Processed 9000 contigs out of 102461 , while untangling with long reads Processed 10000 contigs out of 102461 , while untangling with long reads Processed 11000 contigs out of 102461 , while untangling with long reads Processed 12000 contigs out of 102461 , while untangling with long reads Processed 13000 contigs out of 102461 , while untangling with long reads Processed 14000 contigs out of 102461 , while untangling with long reads Processed 15000 contigs out of 102461 , while untangling with long reads Debug WARNING, ['4229900', '16324833', '16324841', '16324849', '16324859', '16324867', '16324873', '16324879', '16324885', '16324897', '16324903', '16472453', '16445741', '16445753', '16445759', '16445765', '16538773', '16538779', '16538787', '16538797', '16538803', '16538809', '81112111', '16538809', '53260245', '82122851', '6222572', '4773173'] : looking for ['81112111'] 0 from ['16538809'] among [['81112111'], ['16538817']] [1, 0] 4229900 >16324833>16324841>16324849>16324859>16324867>16324873>16324879>16324885>16324897>16324903>16472453>16445741>16445753>16445759>16445765>16538773>16538779>16538787>16538797>16538803>16538809>81112111<16538809<53260245<82122851<6222572>4773173 Processed 16000 contigs out of 102461 , while untangling with long reads Processed 17000 contigs out of 102461 , while untangling with long reads Processed 18000 contigs out of 102461 , while untangling with long reads Processed 19000 contigs out of 102461 , while untangling with long reads Processed 20000 contigs out of 102461 , while untangling with long reads Processed 21000 contigs out of 102461 , while untangling with long reads Processed 22000 contigs out of 102461 , while untangling with long reads Processed 23000 contigs out of 102461 , while untangling with long reads Processed 24000 contigs out of 102461 , while untangling with long reads Processed 25000 contigs out of 102461 , while untangling with long reads Processed 26000 contigs out of 102461 , while untangling with long reads Traceback (most recent call last): File "/Users/jff/.local/bin/graphunzip.py", line 335, in main() File "/Users/jff/.local/bin/graphunzip.py", line 312, in main bridge_with_long_reads(segments, names, cn, lrFile, supported_links2, refHaploidy, multiplicities) File "/Users/jff/.local/src/GraphUnzip/solve_with_long_reads.py", line 120, in bridge_with_long_reads unzip_graph_with_bridges(segments, non_overlapping_bridges, copiesnumber, haploidContigs, haploidContigsNames, names, supported_links2, minimum_supported_links, multiplicities, longContigs) File "/Users/jff/.local/src/GraphUnzip/solve_with_long_reads.py", line 436, in unzip_graph_with_bridges CIGAR = segments[names[contigs[0]]].CIGARs[end][segment.find_this_link(segments[oldContigsIndices[1]], nextEnd, segments[names[contigs[0]]].links[end], segments[names[contigs[0]]].otherEndOfLinks[end])] IndexError: list index out of range

nadegeguiglielmoni / GraphUnzip

GraphUnzip crashed #12