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| 2020-05-05_15-05-54.966462: INFO : Log started: (test_outputs/2020-05-05_15-05-54.966462_log.txt) | ||
| 2020-05-05_15:05:54.967995: INFO : SNPPar: Parallel SNP Finder V0.4.1dev | ||
| (utilising TreeTime for ASR and intermediate sorting) | ||
| 2020-05-05_15:05:54.968403: INFO : User command: snppar -s MTB_Global_L2_alleles.csv -t MTB_Global_L2.tre -g NC_00962_3_1.gbk -d test_outputs | ||
| 2020-05-05_15:05:54.968667: INFO : Reading SNP table from MTB_Global_L2_alleles.csv | ||
| 2020-05-05_15:05:55.132750: INFO : Finished reading 4401 SNPs in total | ||
| ...keeping 4401 variable SNPs and ignoring 0 SNPs | ||
| that are non-variable among the 94 isolates | ||
| 2020-05-05_15:05:55.133277: INFO : Reading Genbank file from NC_00962_3_1.gbk | ||
| 2020-05-05_15:05:56.023196: INFO : Found 3906 genes | ||
| 2020-05-05_15:05:56.023646: INFO : Reading tree from MTB_Global_L2.tre... | ||
| 2020-05-05_15:05:56.032251: INFO : Tree and SNP table have same isolates | ||
| 2020-05-05_15:05:56.032629: INFO : Parsing SNPs to find bi-, tri- and quadallelic SNPs... | ||
| Also testing if biallelic SNPs are homoplasic | ||
| 2020-05-05_15:05:57.227237: INFO : Biallelic SNPs (>1 one isolate): 1440 | ||
| Biallelic SNPs (>1 one isolate, no missing calls): 1440 | ||
| Biallelic SNP patterns tested (no missing calls): 51 | ||
| Paraphyletic SNPs found: 2 | ||
| Triallelic SNPs found: 0 | ||
| Quadallelic SNPs found: 0 | ||
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| Total SNPs for mapping: 2 | ||
| 2020-05-05_15:05:57.228455: INFO : Assigning monophyletic SNPs to genes | ||
| 2020-05-05_15:05:57.247711: INFO : Of the 4399 monophyletic SNPs for testing, 489 are intergenic, and 3922 are intragenic | ||
| 2020-05-05_15:05:57.248047: INFO : 12 SNPs occur in overlapping genes | ||
| 2020-05-05_15:05:57.266262: INFO : Assigning SNPs to map to genes | ||
| 2020-05-05_15:05:57.266846: INFO : Of the 2 SNPs to map for testing, 0 are intergenic, and 2 are intragenic | ||
| 2020-05-05_15:05:57.268311: INFO : Running TreeTime: treetime ancestral --aln test_outputs/snps_to_map.mfasta --tree MTB_Global_L2.tre --outdir test_outputs/treetime_out/ --report-ambiguous --verbose 2 | ||
| 2020-05-05_15:06:00.089242: INFO : stdout: | ||
| 0.00 -TreeAnc: set-up | ||
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| Inferred sequence evolution model (saved as test_outputs/treetime_out//sequence_evolution_model.txt): | ||
| Substitution rate (mu): 1.0 | ||
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| Equilibrium frequencies (pi_i): | ||
| A: 0.2525 | ||
| C: 0.2549 | ||
| G: 0.2413 | ||
| T: 0.2392 | ||
| -: 0.0121 | ||
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| Symmetrized rates from j->i (W_ij): | ||
| A C G T - | ||
| A 0 1.2405 1.4918 1.2434 1.2436 | ||
| C 1.2405 0 1.2429 1.4918 1.2434 | ||
| G 1.4918 1.2429 0 1.2455 1.2456 | ||
| T 1.2434 1.4918 1.2455 0 1.2458 | ||
| - 1.2436 1.2434 1.2456 1.2458 0 | ||
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| Actual rates from j->i (Q_ij): | ||
| A C G T - | ||
| A 0 0.3132 0.3767 0.3139 0.314 | ||
| C 0.3162 0 0.3168 0.3803 0.317 | ||
| G 0.3599 0.2999 0 0.3005 0.3005 | ||
| T 0.2974 0.3568 0.2979 0 0.298 | ||
| - 0.015 0.015 0.0151 0.0151 0 | ||
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| --- alignment including ancestral nodes saved as | ||
| test_outputs/treetime_out/ancestral_sequences.fasta | ||
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| --- tree saved in nexus format as | ||
| test_outputs/treetime_out/annotated_tree.nexus | ||
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| 2020-05-05_15:06:00.090033: INFO : Extracting mutation events from ASR results... | ||
| 2020-05-05_15:06:00.093463: INFO : Extracting internal node sequences from ASR results... | ||
| 2020-05-05_15:06:00.095357: INFO : Processing mapped mutation events... | ||
| 2020-05-05_15:06:00.095687: INFO : Processing monophyletic mutation events... | ||
| 2020-05-05_15:06:01.889402: INFO : Combining monophyletic and mapped mutation events | ||
| Also combining monophyletic and mapped node sequences... | ||
| 2020-05-05_15:06:01.897686: INFO : Writing node sequences to test_outputs/node_sequences.fasta | ||
| 2020-05-05_15:06:02.036351: INFO : Assigning coding consequenses to the mutation events... | ||
| 2020-05-05_15:06:03.249957: INFO : 2855 non-synonymous changes, 1071 synonymous changes, and 489 SNP events in non-coding regions | ||
| 2020-05-05_15:06:03.250475: INFO : Parsing all mutation events... | ||
| 2020-05-05_15:06:03.253026: INFO : Found 4 mutation events that are homoplasic | ||
| 2020-05-05_15:06:03.253422: INFO : Writing all calls at homoplasic event positions to test_outputs/homoplasic_events_all_calls.tsv | ||
| 2020-05-05_15:06:03.258145: INFO : Writing all mutation events to test_outputs/all_mutation_events.tsv | ||
| 2020-05-05_15:06:03.479074: INFO : Mapping mutation events to NEXUS tree: test_outputs/node_labelled_nexus.tre | ||
| 2020-05-05_15:06:03.484283: INFO : Also mapping mutation events to Newick NHX tree: test_outputs/node_labelled_newick.tre | ||
| 2020-05-05_15:06:03.487913: INFO : Cleaning up intermediate files... | ||
| 2020-05-05_15:06:03.502712: INFO : ...Finished |