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/30063225/sequence.fasta /tmp/hivtrace-saosojjr/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-saosojjr/sequence.fasta_output.bam /tmp/hivtrace-saosojjr/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-saosojjr/sequence.fasta_user.tn93output.csv -t 0.015 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-saosojjr/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-saosojjr/sequence.fasta_user.tn93output.csv -t 0.015 -f plain -J -q -n remove -s /tmp/hivtrace-saosojjr/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 80 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 80 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 filtered edges\nFiltering a set of 792 edges (80/80 clusters). Pass 2, 1760 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 filtered edges\nFiltering a set of 792 edges (80/80 clusters). Pass 2, 1760 triangles, 6 filtered edges\nFiltering a set of 786 edges (80/80 clusters). Pass 3, 1709 triangles, 10 filtered edges\n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 filtered edges\nFiltering a set of 792 edges (80/80 clusters). Pass 2, 1760 triangles, 6 filtered edges\nFiltering a set of 786 edges (80/80 clusters). Pass 3, 1709 triangles, 10 filtered edges\nFiltering a set of 776 edges (80/80 clusters). Pass 4, 1680 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 filtered edges\nFiltering a set of 792 edges (80/80 clusters). Pass 2, 1760 triangles, 6 filtered edges\nFiltering a set of 786 edges (80/80 clusters). Pass 3, 1709 triangles, 10 filtered edges\nFiltering a set of 776 edges (80/80 clusters). Pass 4, 1680 triangles, 0 filtered edges\nEdge filtering identified 149 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 filtered edges\nFiltering a set of 792 edges (80/80 clusters). Pass 2, 1760 triangles, 6 filtered edges\nFiltering a set of 786 edges (80/80 clusters). Pass 3, 1709 triangles, 10 filtered edges\nFiltering a set of 776 edges (80/80 clusters). Pass 4, 1680 triangles, 0 filtered edges\nEdge filtering identified 149 edges for removal\nEdge filtering removed 149 edges\n"} INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 filtered edges\nFiltering a set of 792 edges (80/80 clusters). Pass 2, 1760 triangles, 6 filtered edges\nFiltering a set of 786 edges (80/80 clusters). Pass 3, 1709 triangles, 10 filtered edges\nFiltering a set of 776 edges (80/80 clusters). Pass 4, 1680 triangles, 0 filtered edges\nEdge filtering identified 149 edges for removal\nEdge filtering removed 149 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 80 clusters with 3 or more edges\n\nFiltering a set of 595 edges (73/80 clusters) \nFiltering a set of 595 edges (73/80 clusters). Pass 0, 501 triangles, 75 filtered edges\nFiltering a set of 520 edges (73/80 clusters). Pass 1, 143 triangles, 5 filtered edges\nFiltering a set of 515 edges (73/80 clusters). Pass 2, 136 triangles, 0 filtered edges\nFiltering a set of 138 edges (74/80 clusters) \nFiltering a set of 138 edges (74/80 clusters). Pass 0, 554 triangles, 0 filtered edges\nFiltering a set of 164 edges (75/80 clusters) \nFiltering a set of 164 edges (75/80 clusters). Pass 0, 841 triangles, 1 filtered edges\nFiltering a set of 163 edges (75/80 clusters). Pass 1, 40 triangles, 0 filtered edges\nFiltering a set of 178 edges (76/80 clusters) \nFiltering a set of 178 edges (76/80 clusters). Pass 0, 314 triangles, 0 filtered edges\nFiltering a set of 224 edges (77/80 clusters) \nFiltering a set of 224 edges (77/80 clusters). Pass 0, 1090 triangles, 0 filtered edges\nFiltering a set of 283 edges (78/80 clusters) \nFiltering a set of 283 edges (78/80 clusters). Pass 0, 1684 triangles, 5 filtered edges\nFiltering a set of 278 edges (78/80 clusters). Pass 1, 739 triangles, 0 filtered edges\nFiltering a set of 594 edges (79/80 clusters) \nFiltering a set of 594 edges (79/80 clusters). Pass 0, 4643 triangles, 0 filtered edges\nFiltering a set of 839 edges (80/80 clusters) \nFiltering a set of 839 edges (80/80 clusters). Pass 0, 3175 triangles, 34 filtered edges\nFiltering a set of 805 edges (80/80 clusters). Pass 1, 1812 triangles, 13 filtered edges\nFiltering a set of 792 edges (80/80 clusters). Pass 2, 1760 triangles, 6 filtered edges\nFiltering a set of 786 edges (80/80 clusters). Pass 3, 1709 triangles, 10 filtered edges\nFiltering a set of 776 edges (80/80 clusters). Pass 4, 1680 triangles, 0 filtered edges\nEdge filtering identified 149 edges for removal\nEdge filtering removed 149 edges\nFitting the degree distribution to various densities\n"}