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-htzzw1xg/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-htzzw1xg/sequence.fasta_output.bam /tmp/hivtrace-htzzw1xg/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-htzzw1xg/sequence.fasta_user.tn93output.csv -t 0.00676 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-htzzw1xg/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-htzzw1xg/sequence.fasta_user.tn93output.csv -t 0.00676 -f plain -J -q -n remove -s /tmp/hivtrace-htzzw1xg/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 52 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 52 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 triangles, 1 filtered edges\nFiltering a set of 539 edges (52/52 clusters). Pass 3, 141 triangles, 2 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 triangles, 1 filtered edges\nFiltering a set of 539 edges (52/52 clusters). Pass 3, 141 triangles, 2 filtered edges\nFiltering a set of 537 edges (52/52 clusters). Pass 4, 139 triangles, 2 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 triangles, 1 filtered edges\nFiltering a set of 539 edges (52/52 clusters). Pass 3, 141 triangles, 2 filtered edges\nFiltering a set of 537 edges (52/52 clusters). Pass 4, 139 triangles, 2 filtered edges\nFiltering a set of 535 edges (52/52 clusters). Pass 5, 138 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 triangles, 1 filtered edges\nFiltering a set of 539 edges (52/52 clusters). Pass 3, 141 triangles, 2 filtered edges\nFiltering a set of 537 edges (52/52 clusters). Pass 4, 139 triangles, 2 filtered edges\nFiltering a set of 535 edges (52/52 clusters). Pass 5, 138 triangles, 0 filtered edges\nEdge filtering identified 582 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 triangles, 1 filtered edges\nFiltering a set of 539 edges (52/52 clusters). Pass 3, 141 triangles, 2 filtered edges\nFiltering a set of 537 edges (52/52 clusters). Pass 4, 139 triangles, 2 filtered edges\nFiltering a set of 535 edges (52/52 clusters). Pass 5, 138 triangles, 0 filtered edges\nEdge filtering identified 582 edges for removal\nEdge filtering removed 582 edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 triangles, 1 filtered edges\nFiltering a set of 539 edges (52/52 clusters). Pass 3, 141 triangles, 2 filtered edges\nFiltering a set of 537 edges (52/52 clusters). Pass 4, 139 triangles, 2 filtered edges\nFiltering a set of 535 edges (52/52 clusters). Pass 5, 138 triangles, 0 filtered edges\nEdge filtering identified 582 edges for removal\nEdge filtering removed 582 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 52 clusters with 3 or more edges\n\nFiltering a set of 532 edges (50/52 clusters)                                                                                 \nFiltering a set of 532 edges (50/52 clusters). Pass 0, 528 triangles, 137 filtered edges\nFiltering a set of 395 edges (50/52 clusters). Pass 1, 130 triangles, 2 filtered edges\nFiltering a set of 393 edges (50/52 clusters). Pass 2, 123 triangles, 1 filtered edges\nFiltering a set of 392 edges (50/52 clusters). Pass 3, 118 triangles, 1 filtered edges\nFiltering a set of 391 edges (50/52 clusters). Pass 4, 114 triangles, 1 filtered edges\nFiltering a set of 390 edges (50/52 clusters). Pass 5, 111 triangles, 1 filtered edges\nFiltering a set of 389 edges (50/52 clusters). Pass 6, 109 triangles, 1 filtered edges\nFiltering a set of 388 edges (50/52 clusters). Pass 7, 108 triangles, 0 filtered edges\nFiltering a set of 130 edges (51/52 clusters)                                                                                 \nFiltering a set of 130 edges (51/52 clusters). Pass 0, 527 triangles, 52 filtered edges\nFiltering a set of 78 edges (51/52 clusters). Pass 1, 156 triangles, 4 filtered edges\nFiltering a set of 74 edges (51/52 clusters). Pass 2, 138 triangles, 5 filtered edges\nFiltering a set of 69 edges (51/52 clusters). Pass 3, 125 triangles, 6 filtered edges\nFiltering a set of 63 edges (51/52 clusters). Pass 4, 116 triangles, 0 filtered edges\nFiltering a set of 906 edges (52/52 clusters)                                                                                 \nFiltering a set of 906 edges (52/52 clusters). Pass 0, 1898 triangles, 347 filtered edges\nFiltering a set of 559 edges (52/52 clusters). Pass 1, 183 triangles, 19 filtered edges\nFiltering a set of 540 edges (52/52 clusters). Pass 2, 144 triangles, 1 filtered edges\nFiltering a set of 539 edges (52/52 clusters). Pass 3, 141 triangles, 2 filtered edges\nFiltering a set of 537 edges (52/52 clusters). Pass 4, 139 triangles, 2 filtered edges\nFiltering a set of 535 edges (52/52 clusters). Pass 5, 138 triangles, 0 filtered edges\nEdge filtering identified 582 edges for removal\nEdge filtering removed 582 edges\nFitting the degree distribution to various densities\n"}