INFO:root:{"type": "status update", "index": 0, "title": "Aligning", "status": 2, "msg": ""}
DEBUG:root:/home/sweaver/programming/hivtrace/env39/bin/bealign -q -r ./rsrc/ref.fasta -m HIV_BETWEEN_F -R rsrc/papers/22739398/sequence.fasta /tmp/hivtrace-ei75y115/sequence.fasta_output.bam
INFO:root:{"type": "status update", "index": 0, "title": "Aligning", "status": 3, "msg": ""}
INFO:root:{"type": "status update", "index": 1, "title": "BAM to FASTA conversion", "status": 2, "msg": ""}
DEBUG:root:/home/sweaver/programming/hivtrace/env39/bin/bam2msa /tmp/hivtrace-ei75y115/sequence.fasta_output.bam /tmp/hivtrace-ei75y115/sequence.fasta_output.fasta
INFO:root:{"type": "status update", "index": 1, "title": "BAM to FASTA conversion", "status": 3, "msg": ""}
INFO:root:{"type": "status update", "index": 3, "title": "Computing pairwise TN93 distances", "status": 2, "msg": ""}
DEBUG:root:tn93 -q -0 -o /tmp/hivtrace-ei75y115/sequence.fasta_user.tn93output.csv -t 0.01283 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-ei75y115/sequence.fasta_output.fasta
INFO:root:{"type": "status update", "index": 3, "title": "Computing pairwise TN93 distances", "status": 3, "msg": ""}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": ""}
DEBUG:root:/home/sweaver/programming/hivtrace/env39/bin/hivnetworkcsv -i /tmp/hivtrace-ei75y115/sequence.fasta_user.tn93output.csv -t 0.01283 -f plain -J -q -n remove -s /tmp/hivtrace-ei75y115/sequence.fasta_output.fasta -l --cycle-report-file data/hivtrace/22739398_nodes.cycle_report.json
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\nFiltering a set of 77 edges (10/10 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\nFiltering a set of 77 edges (10/10 clusters)                                                                                 \nFiltering a set of 77 edges (10/10 clusters). Pass 0, 85 triangles, 5 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\nFiltering a set of 77 edges (10/10 clusters)                                                                                 \nFiltering a set of 77 edges (10/10 clusters). Pass 0, 85 triangles, 5 filtered edges\n4-cycle filtering a set of 72 edges (10/10 clusters). Pass 0, 199 4-cycles, 0 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\nFiltering a set of 77 edges (10/10 clusters)                                                                                 \nFiltering a set of 77 edges (10/10 clusters). Pass 0, 85 triangles, 5 filtered edges\n4-cycle filtering a set of 72 edges (10/10 clusters). Pass 0, 199 4-cycles, 0 filtered edges\nEdge filtering identified 5 edges for removal\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\nFiltering a set of 77 edges (10/10 clusters)                                                                                 \nFiltering a set of 77 edges (10/10 clusters). Pass 0, 85 triangles, 5 filtered edges\n4-cycle filtering a set of 72 edges (10/10 clusters). Pass 0, 199 4-cycles, 0 filtered edges\nEdge filtering identified 5 edges for removal\nEdge filtering removed 5 edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\nFiltering a set of 77 edges (10/10 clusters)                                                                                 \nFiltering a set of 77 edges (10/10 clusters). Pass 0, 85 triangles, 5 filtered edges\n4-cycle filtering a set of 72 edges (10/10 clusters). Pass 0, 199 4-cycles, 0 filtered edges\nEdge filtering identified 5 edges for removal\nEdge filtering removed 5 edges\nFitting the degree distribution to various densities\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 3, "msg": "Running edge filtering on 10 clusters with 3 or more edges\n\nFiltering a set of 77 edges (10/10 clusters)                                                                                 \nFiltering a set of 77 edges (10/10 clusters). Pass 0, 85 triangles, 5 filtered edges\n4-cycle filtering a set of 72 edges (10/10 clusters). Pass 0, 199 4-cycles, 0 filtered edges\nEdge filtering identified 5 edges for removal\nEdge filtering removed 5 edges\nFitting the degree distribution to various densities\n"}