INFO:root:{"type": "status update", "index": 0, "title": "Aligning", "status": 2, "msg": ""}
DEBUG:root:/opt/edge-filtering/edge/bin/bealign -q -r HXB2_prrt -m HIV_BETWEEN_F -R data/seq_gen/C.Epidemic.fas /tmp/hivtrace-s9vgv5us/C.Epidemic.fas_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:/opt/edge-filtering/edge/bin/bam2msa /tmp/hivtrace-s9vgv5us/C.Epidemic.fas_output.bam /tmp/hivtrace-s9vgv5us/C.Epidemic.fas_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 -o /tmp/hivtrace-s9vgv5us/C.Epidemic.fas_user.tn93output.csv -t .015 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-s9vgv5us/C.Epidemic.fas_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:/opt/edge-filtering/edge/bin/hivnetworkcsv -i /tmp/hivtrace-s9vgv5us/C.Epidemic.fas_user.tn93output.csv -t .015 -f plain -j -o -n remove -s /tmp/hivtrace-s9vgv5us/C.Epidemic.fas_output.fasta -l --cycle-report-file data/hivtrace/C.Epidemic_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 2 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 2 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 filtered edges\n4-cycle filtering a set of 2313 edges (2/2 clusters). Pass 1, 65538 4-cycles, 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 filtered edges\n4-cycle filtering a set of 2313 edges (2/2 clusters). Pass 1, 65538 4-cycles, 5 filtered edges\n4-cycle filtering a set of 2308 edges (2/2 clusters). Pass 2, 78157 4-cycles, 2 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 filtered edges\n4-cycle filtering a set of 2313 edges (2/2 clusters). Pass 1, 65538 4-cycles, 5 filtered edges\n4-cycle filtering a set of 2308 edges (2/2 clusters). Pass 2, 78157 4-cycles, 2 filtered edges\n4-cycle filtering a set of 2306 edges (2/2 clusters). Pass 3, 69968 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 filtered edges\n4-cycle filtering a set of 2313 edges (2/2 clusters). Pass 1, 65538 4-cycles, 5 filtered edges\n4-cycle filtering a set of 2308 edges (2/2 clusters). Pass 2, 78157 4-cycles, 2 filtered edges\n4-cycle filtering a set of 2306 edges (2/2 clusters). Pass 3, 69968 4-cycles, 0 filtered edges\nEdge filtering identified 810 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 filtered edges\n4-cycle filtering a set of 2313 edges (2/2 clusters). Pass 1, 65538 4-cycles, 5 filtered edges\n4-cycle filtering a set of 2308 edges (2/2 clusters). Pass 2, 78157 4-cycles, 2 filtered edges\n4-cycle filtering a set of 2306 edges (2/2 clusters). Pass 3, 69968 4-cycles, 0 filtered edges\nEdge filtering identified 810 edges for removal\nEdge filtering removed 810 edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 filtered edges\n4-cycle filtering a set of 2313 edges (2/2 clusters). Pass 1, 65538 4-cycles, 5 filtered edges\n4-cycle filtering a set of 2308 edges (2/2 clusters). Pass 2, 78157 4-cycles, 2 filtered edges\n4-cycle filtering a set of 2306 edges (2/2 clusters). Pass 3, 69968 4-cycles, 0 filtered edges\nEdge filtering identified 810 edges for removal\nEdge filtering removed 810 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 2 clusters with 3 or more edges\n\nFiltering a set of 3116 edges (2/2 clusters)                                                                                 \nFiltering a set of 3116 edges (2/2 clusters). Pass 0, 15175 triangles, 793 filtered edges\nFiltering a set of 2323 edges (2/2 clusters). Pass 1, 17 triangles, 4 filtered edges\nFiltering a set of 2319 edges (2/2 clusters). Pass 2, 11 triangles, 0 filtered edges\n4-cycle filtering a set of 2319 edges (2/2 clusters). Pass 0, 32783 4-cycles, 6 filtered edges\n4-cycle filtering a set of 2313 edges (2/2 clusters). Pass 1, 65538 4-cycles, 5 filtered edges\n4-cycle filtering a set of 2308 edges (2/2 clusters). Pass 2, 78157 4-cycles, 2 filtered edges\n4-cycle filtering a set of 2306 edges (2/2 clusters). Pass 3, 69968 4-cycles, 0 filtered edges\nEdge filtering identified 810 edges for removal\nEdge filtering removed 810 edges\nFitting the degree distribution to various densities\n"}