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/33901684/sequence.fasta /tmp/hivtrace-_ts17w8z/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-_ts17w8z/sequence.fasta_output.bam /tmp/hivtrace-_ts17w8z/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-_ts17w8z/sequence.fasta_user.tn93output.csv -t 0.01215 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-_ts17w8z/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-_ts17w8z/sequence.fasta_user.tn93output.csv -t 0.01215 -f plain -J -q -n remove -s /tmp/hivtrace-_ts17w8z/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 42 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 42 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 filtered edges\nFiltering a set of 8697 edges (42/42 clusters). Pass 3, 41360 triangles, 626 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 filtered edges\nFiltering a set of 8697 edges (42/42 clusters). Pass 3, 41360 triangles, 626 filtered edges\nFiltering a set of 8071 edges (42/42 clusters). Pass 4, 836 triangles, 20 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 filtered edges\nFiltering a set of 8697 edges (42/42 clusters). Pass 3, 41360 triangles, 626 filtered edges\nFiltering a set of 8071 edges (42/42 clusters). Pass 4, 836 triangles, 20 filtered edges\nFiltering a set of 8051 edges (42/42 clusters). Pass 5, 810 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 filtered edges\nFiltering a set of 8697 edges (42/42 clusters). Pass 3, 41360 triangles, 626 filtered edges\nFiltering a set of 8071 edges (42/42 clusters). Pass 4, 836 triangles, 20 filtered edges\nFiltering a set of 8051 edges (42/42 clusters). Pass 5, 810 triangles, 0 filtered edges\nEdge filtering identified 5004 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 filtered edges\nFiltering a set of 8697 edges (42/42 clusters). Pass 3, 41360 triangles, 626 filtered edges\nFiltering a set of 8071 edges (42/42 clusters). Pass 4, 836 triangles, 20 filtered edges\nFiltering a set of 8051 edges (42/42 clusters). Pass 5, 810 triangles, 0 filtered edges\nEdge filtering identified 5004 edges for removal\nEdge filtering removed 5004 edges\n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 filtered edges\nFiltering a set of 8697 edges (42/42 clusters). Pass 3, 41360 triangles, 626 filtered edges\nFiltering a set of 8071 edges (42/42 clusters). Pass 4, 836 triangles, 20 filtered edges\nFiltering a set of 8051 edges (42/42 clusters). Pass 5, 810 triangles, 0 filtered edges\nEdge filtering identified 5004 edges for removal\nEdge filtering removed 5004 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 42 clusters with 3 or more edges\n\nFiltering a set of 346 edges (37/42 clusters) \nFiltering a set of 346 edges (37/42 clusters). Pass 0, 470 triangles, 96 filtered edges\nFiltering a set of 250 edges (37/42 clusters). Pass 1, 18 triangles, 1 filtered edges\nFiltering a set of 249 edges (37/42 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 67 edges (38/42 clusters) \nFiltering a set of 67 edges (38/42 clusters). Pass 0, 220 triangles, 39 filtered edges\nFiltering a set of 28 edges (38/42 clusters). Pass 1, 10 triangles, 1 filtered edges\nFiltering a set of 27 edges (38/42 clusters). Pass 2, 9 triangles, 0 filtered edges\nFiltering a set of 86 edges (39/42 clusters) \nFiltering a set of 86 edges (39/42 clusters). Pass 0, 253 triangles, 21 filtered edges\nFiltering a set of 434 edges (40/42 clusters) \nFiltering a set of 434 edges (40/42 clusters). Pass 0, 2123 triangles, 69 filtered edges\nFiltering a set of 5989 edges (41/42 clusters) \nFiltering a set of 5989 edges (41/42 clusters). Pass 0, 32768 triangles, 337 filtered edges\nFiltering a set of 5652 edges (41/42 clusters). Pass 1, 65536 triangles, 669 filtered edges\nFiltering a set of 4983 edges (41/42 clusters). Pass 2, 60523 triangles, 813 filtered edges\nFiltering a set of 4170 edges (41/42 clusters). Pass 3, 190 triangles, 18 filtered edges\nFiltering a set of 4152 edges (41/42 clusters). Pass 4, 169 triangles, 0 filtered edges\nFiltering a set of 10991 edges (42/42 clusters) \nFiltering a set of 10991 edges (42/42 clusters). Pass 0, 32768 triangles, 191 filtered edges\nFiltering a set of 10800 edges (42/42 clusters). Pass 1, 65536 triangles, 736 filtered edges\nFiltering a set of 10064 edges (42/42 clusters). Pass 2, 98304 triangles, 1367 filtered edges\nFiltering a set of 8697 edges (42/42 clusters). Pass 3, 41360 triangles, 626 filtered edges\nFiltering a set of 8071 edges (42/42 clusters). Pass 4, 836 triangles, 20 filtered edges\nFiltering a set of 8051 edges (42/42 clusters). Pass 5, 810 triangles, 0 filtered edges\nEdge filtering identified 5004 edges for removal\nEdge filtering removed 5004 edges\nFitting the degree distribution to various densities\n"}