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/33281803/sequence.fasta /tmp/hivtrace-ganw5l4l/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-ganw5l4l/sequence.fasta_output.bam /tmp/hivtrace-ganw5l4l/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-ganw5l4l/sequence.fasta_user.tn93output.csv -t 0.015 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-ganw5l4l/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-ganw5l4l/sequence.fasta_user.tn93output.csv -t 0.015 -f plain -J -q -n remove -s /tmp/hivtrace-ganw5l4l/sequence.fasta_output.fasta INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 23 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 23 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 filtered edges\nFiltering a set of 14372 edges (23/23 clusters). Pass 5, 1572 triangles, 77 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 filtered edges\nFiltering a set of 14372 edges (23/23 clusters). Pass 5, 1572 triangles, 77 filtered edges\nFiltering a set of 14295 edges (23/23 clusters). Pass 6, 1433 triangles, 27 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 filtered edges\nFiltering a set of 14372 edges (23/23 clusters). Pass 5, 1572 triangles, 77 filtered edges\nFiltering a set of 14295 edges (23/23 clusters). Pass 6, 1433 triangles, 27 filtered edges\nFiltering a set of 14268 edges (23/23 clusters). Pass 7, 1399 triangles, 8 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 filtered edges\nFiltering a set of 14372 edges (23/23 clusters). Pass 5, 1572 triangles, 77 filtered edges\nFiltering a set of 14295 edges (23/23 clusters). Pass 6, 1433 triangles, 27 filtered edges\nFiltering a set of 14268 edges (23/23 clusters). Pass 7, 1399 triangles, 8 filtered edges\nEdge filtering identified 13506 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 filtered edges\nFiltering a set of 14372 edges (23/23 clusters). Pass 5, 1572 triangles, 77 filtered edges\nFiltering a set of 14295 edges (23/23 clusters). Pass 6, 1433 triangles, 27 filtered edges\nFiltering a set of 14268 edges (23/23 clusters). Pass 7, 1399 triangles, 8 filtered edges\nEdge filtering identified 13506 edges for removal\nEdge filtering removed 13506 edges\n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 filtered edges\nFiltering a set of 14372 edges (23/23 clusters). Pass 5, 1572 triangles, 77 filtered edges\nFiltering a set of 14295 edges (23/23 clusters). Pass 6, 1433 triangles, 27 filtered edges\nFiltering a set of 14268 edges (23/23 clusters). Pass 7, 1399 triangles, 8 filtered edges\nEdge filtering identified 13506 edges for removal\nEdge filtering removed 13506 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 23 clusters with 3 or more edges\n\nFiltering a set of 451 edges (21/23 clusters) \nFiltering a set of 451 edges (21/23 clusters). Pass 0, 1190 triangles, 199 filtered edges\nFiltering a set of 252 edges (21/23 clusters). Pass 1, 119 triangles, 8 filtered edges\nFiltering a set of 244 edges (21/23 clusters). Pass 2, 107 triangles, 1 filtered edges\nFiltering a set of 243 edges (21/23 clusters). Pass 3, 102 triangles, 1 filtered edges\nFiltering a set of 242 edges (21/23 clusters). Pass 4, 98 triangles, 1 filtered edges\nFiltering a set of 241 edges (21/23 clusters). Pass 5, 95 triangles, 1 filtered edges\nFiltering a set of 240 edges (21/23 clusters). Pass 6, 93 triangles, 1 filtered edges\nFiltering a set of 239 edges (21/23 clusters). Pass 7, 92 triangles, 0 filtered edges\nFiltering a set of 406 edges (22/23 clusters) \nFiltering a set of 406 edges (22/23 clusters). Pass 0, 1594 triangles, 115 filtered edges\nFiltering a set of 291 edges (22/23 clusters). Pass 1, 30 triangles, 8 filtered edges\nFiltering a set of 283 edges (22/23 clusters). Pass 2, 22 triangles, 0 filtered edges\nFiltering a set of 27431 edges (23/23 clusters) \nFiltering a set of 27431 edges (23/23 clusters). Pass 0, 32768 triangles, 628 filtered edges\nFiltering a set of 26803 edges (23/23 clusters). Pass 1, 65536 triangles, 1338 filtered edges\nFiltering a set of 25465 edges (23/23 clusters). Pass 2, 98304 triangles, 4126 filtered edges\nFiltering a set of 21339 edges (23/23 clusters). Pass 3, 131072 triangles, 4740 filtered edges\nFiltering a set of 16599 edges (23/23 clusters). Pass 4, 41914 triangles, 2227 filtered edges\nFiltering a set of 14372 edges (23/23 clusters). Pass 5, 1572 triangles, 77 filtered edges\nFiltering a set of 14295 edges (23/23 clusters). Pass 6, 1433 triangles, 27 filtered edges\nFiltering a set of 14268 edges (23/23 clusters). Pass 7, 1399 triangles, 8 filtered edges\nEdge filtering identified 13506 edges for removal\nEdge filtering removed 13506 edges\nFitting the degree distribution to various densities\n"}