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/32500089/sequence.fasta /tmp/hivtrace-fddevc3z/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-fddevc3z/sequence.fasta_output.bam /tmp/hivtrace-fddevc3z/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-fddevc3z/sequence.fasta_user.tn93output.csv -t 0.00675 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-fddevc3z/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-fddevc3z/sequence.fasta_user.tn93output.csv -t 0.00675 -f plain -J -q -n remove -s /tmp/hivtrace-fddevc3z/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 70 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 70 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \nFiltering a set of 1234 edges (70/70 clusters). Pass 0, 7380 triangles, 222 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \nFiltering a set of 1234 edges (70/70 clusters). Pass 0, 7380 triangles, 222 filtered edges\nFiltering a set of 1012 edges (70/70 clusters). Pass 1, 73 triangles, 9 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \nFiltering a set of 1234 edges (70/70 clusters). Pass 0, 7380 triangles, 222 filtered edges\nFiltering a set of 1012 edges (70/70 clusters). Pass 1, 73 triangles, 9 filtered edges\nFiltering a set of 1003 edges (70/70 clusters). Pass 2, 63 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \nFiltering a set of 1234 edges (70/70 clusters). Pass 0, 7380 triangles, 222 filtered edges\nFiltering a set of 1012 edges (70/70 clusters). Pass 1, 73 triangles, 9 filtered edges\nFiltering a set of 1003 edges (70/70 clusters). Pass 2, 63 triangles, 0 filtered edges\nEdge filtering identified 779 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \nFiltering a set of 1234 edges (70/70 clusters). Pass 0, 7380 triangles, 222 filtered edges\nFiltering a set of 1012 edges (70/70 clusters). Pass 1, 73 triangles, 9 filtered edges\nFiltering a set of 1003 edges (70/70 clusters). Pass 2, 63 triangles, 0 filtered edges\nEdge filtering identified 779 edges for removal\nEdge filtering removed 779 edges\n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \nFiltering a set of 1234 edges (70/70 clusters). Pass 0, 7380 triangles, 222 filtered edges\nFiltering a set of 1012 edges (70/70 clusters). Pass 1, 73 triangles, 9 filtered edges\nFiltering a set of 1003 edges (70/70 clusters). Pass 2, 63 triangles, 0 filtered edges\nEdge filtering identified 779 edges for removal\nEdge filtering removed 779 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 70 clusters with 3 or more edges\n\nFiltering a set of 580 edges (64/70 clusters) \nFiltering a set of 580 edges (64/70 clusters). Pass 0, 645 triangles, 129 filtered edges\nFiltering a set of 451 edges (64/70 clusters). Pass 1, 18 triangles, 0 filtered edges\nFiltering a set of 89 edges (65/70 clusters) \nFiltering a set of 89 edges (65/70 clusters). Pass 0, 169 triangles, 12 filtered edges\nFiltering a set of 124 edges (66/70 clusters) \nFiltering a set of 124 edges (66/70 clusters). Pass 0, 563 triangles, 80 filtered edges\nFiltering a set of 44 edges (66/70 clusters). Pass 1, 20 triangles, 3 filtered edges\nFiltering a set of 41 edges (66/70 clusters). Pass 2, 17 triangles, 0 filtered edges\nFiltering a set of 155 edges (67/70 clusters) \nFiltering a set of 155 edges (67/70 clusters). Pass 0, 483 triangles, 0 filtered edges\nFiltering a set of 181 edges (68/70 clusters) \nFiltering a set of 181 edges (68/70 clusters). Pass 0, 959 triangles, 119 filtered edges\nFiltering a set of 62 edges (68/70 clusters). Pass 1, 19 triangles, 3 filtered edges\nFiltering a set of 59 edges (68/70 clusters). Pass 2, 16 triangles, 0 filtered edges\nFiltering a set of 905 edges (69/70 clusters) \nFiltering a set of 905 edges (69/70 clusters). Pass 0, 1558 triangles, 190 filtered edges\nFiltering a set of 715 edges (69/70 clusters). Pass 1, 44 triangles, 12 filtered edges\nFiltering a set of 703 edges (69/70 clusters). Pass 2, 32 triangles, 0 filtered edges\nFiltering a set of 1234 edges (70/70 clusters) \nFiltering a set of 1234 edges (70/70 clusters). Pass 0, 7380 triangles, 222 filtered edges\nFiltering a set of 1012 edges (70/70 clusters). Pass 1, 73 triangles, 9 filtered edges\nFiltering a set of 1003 edges (70/70 clusters). Pass 2, 63 triangles, 0 filtered edges\nEdge filtering identified 779 edges for removal\nEdge filtering removed 779 edges\nFitting the degree distribution to various densities\n"}