INFO:root:{"type": "status update", "index": 0, "title": "Aligning", "status": 2, "msg": ""} DEBUG:root:/opt/edge-filtering/edge/bin/bealign -q -r ./simulate/hiv.seq.ref.fasta -m HIV_BETWEEN_F -R data/seq_gen/C.Epidemic.fas /tmp/hivtrace-08hf1f0_/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-08hf1f0_/C.Epidemic.fas_output.bam /tmp/hivtrace-08hf1f0_/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-08hf1f0_/C.Epidemic.fas_user.tn93output.csv -t .03 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-08hf1f0_/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-08hf1f0_/C.Epidemic.fas_user.tn93output.csv -t .03 -f plain -j -o -n remove -s /tmp/hivtrace-08hf1f0_/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 1 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 1 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 filtered edges\n4-cycle filtering a set of 37627 edges (1/1 clusters). Pass 5, 196666 4-cycles, 43 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 filtered edges\n4-cycle filtering a set of 37627 edges (1/1 clusters). Pass 5, 196666 4-cycles, 43 filtered edges\n4-cycle filtering a set of 37584 edges (1/1 clusters). Pass 6, 229494 4-cycles, 18 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 filtered edges\n4-cycle filtering a set of 37627 edges (1/1 clusters). Pass 5, 196666 4-cycles, 43 filtered edges\n4-cycle filtering a set of 37584 edges (1/1 clusters). Pass 6, 229494 4-cycles, 18 filtered edges\n4-cycle filtering a set of 37566 edges (1/1 clusters). Pass 7, 262223 4-cycles, 21 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 filtered edges\n4-cycle filtering a set of 37627 edges (1/1 clusters). Pass 5, 196666 4-cycles, 43 filtered edges\n4-cycle filtering a set of 37584 edges (1/1 clusters). Pass 6, 229494 4-cycles, 18 filtered edges\n4-cycle filtering a set of 37566 edges (1/1 clusters). Pass 7, 262223 4-cycles, 21 filtered edges\nEdge filtering identified 2726 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 filtered edges\n4-cycle filtering a set of 37627 edges (1/1 clusters). Pass 5, 196666 4-cycles, 43 filtered edges\n4-cycle filtering a set of 37584 edges (1/1 clusters). Pass 6, 229494 4-cycles, 18 filtered edges\n4-cycle filtering a set of 37566 edges (1/1 clusters). Pass 7, 262223 4-cycles, 21 filtered edges\nEdge filtering identified 2726 edges for removal\nEdge filtering removed 2726 edges\n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 filtered edges\n4-cycle filtering a set of 37627 edges (1/1 clusters). Pass 5, 196666 4-cycles, 43 filtered edges\n4-cycle filtering a set of 37584 edges (1/1 clusters). Pass 6, 229494 4-cycles, 18 filtered edges\n4-cycle filtering a set of 37566 edges (1/1 clusters). Pass 7, 262223 4-cycles, 21 filtered edges\nEdge filtering identified 2726 edges for removal\nEdge filtering removed 2726 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters) \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 25 filtered edges\nFiltering a set of 40246 edges (1/1 clusters). Pass 1, 65536 triangles, 85 filtered edges\nFiltering a set of 40161 edges (1/1 clusters). Pass 2, 98304 triangles, 262 filtered edges\nFiltering a set of 39899 edges (1/1 clusters). Pass 3, 131072 triangles, 151 filtered edges\nFiltering a set of 39748 edges (1/1 clusters). Pass 4, 163840 triangles, 79 filtered edges\nFiltering a set of 39669 edges (1/1 clusters). Pass 5, 196608 triangles, 275 filtered edges\nFiltering a set of 39394 edges (1/1 clusters). Pass 6, 229376 triangles, 303 filtered edges\nFiltering a set of 39091 edges (1/1 clusters). Pass 7, 262144 triangles, 1121 filtered edges\n4-cycle filtering a set of 37970 edges (1/1 clusters). Pass 0, 32809 4-cycles, 207 filtered edges\n4-cycle filtering a set of 37763 edges (1/1 clusters). Pass 1, 65605 4-cycles, 36 filtered edges\n4-cycle filtering a set of 37727 edges (1/1 clusters). Pass 2, 98400 4-cycles, 64 filtered edges\n4-cycle filtering a set of 37663 edges (1/1 clusters). Pass 3, 131081 4-cycles, 26 filtered edges\n4-cycle filtering a set of 37637 edges (1/1 clusters). Pass 4, 163850 4-cycles, 10 filtered edges\n4-cycle filtering a set of 37627 edges (1/1 clusters). Pass 5, 196666 4-cycles, 43 filtered edges\n4-cycle filtering a set of 37584 edges (1/1 clusters). Pass 6, 229494 4-cycles, 18 filtered edges\n4-cycle filtering a set of 37566 edges (1/1 clusters). Pass 7, 262223 4-cycles, 21 filtered edges\nEdge filtering identified 2726 edges for removal\nEdge filtering removed 2726 edges\nFitting the degree distribution to various densities\n"}