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/22484759/sequence.fasta /tmp/hivtrace-_ikc4wiu/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-_ikc4wiu/sequence.fasta_output.bam /tmp/hivtrace-_ikc4wiu/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-_ikc4wiu/sequence.fasta_user.tn93output.csv -t 0.04287 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-_ikc4wiu/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-_ikc4wiu/sequence.fasta_user.tn93output.csv -t 0.04287 -f plain -J -q -n remove -s /tmp/hivtrace-_ikc4wiu/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 8 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 8 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 filtered edges\nFiltering a set of 314 edges (8/8 clusters). Pass 1, 102 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 filtered edges\nFiltering a set of 314 edges (8/8 clusters). Pass 1, 102 triangles, 3 filtered edges\nFiltering a set of 311 edges (8/8 clusters). Pass 2, 96 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 filtered edges\nFiltering a set of 314 edges (8/8 clusters). Pass 1, 102 triangles, 3 filtered edges\nFiltering a set of 311 edges (8/8 clusters). Pass 2, 96 triangles, 2 filtered edges\nFiltering a set of 309 edges (8/8 clusters). Pass 3, 92 triangles, 0 filtered edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 filtered edges\nFiltering a set of 314 edges (8/8 clusters). Pass 1, 102 triangles, 3 filtered edges\nFiltering a set of 311 edges (8/8 clusters). Pass 2, 96 triangles, 2 filtered edges\nFiltering a set of 309 edges (8/8 clusters). Pass 3, 92 triangles, 0 filtered edges\nEdge filtering identified 93 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 filtered edges\nFiltering a set of 314 edges (8/8 clusters). Pass 1, 102 triangles, 3 filtered edges\nFiltering a set of 311 edges (8/8 clusters). Pass 2, 96 triangles, 2 filtered edges\nFiltering a set of 309 edges (8/8 clusters). Pass 3, 92 triangles, 0 filtered edges\nEdge filtering identified 93 edges for removal\nEdge filtering removed 93 edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 filtered edges\nFiltering a set of 314 edges (8/8 clusters). Pass 1, 102 triangles, 3 filtered edges\nFiltering a set of 311 edges (8/8 clusters). Pass 2, 96 triangles, 2 filtered edges\nFiltering a set of 309 edges (8/8 clusters). Pass 3, 92 triangles, 0 filtered edges\nEdge filtering identified 93 edges for removal\nEdge filtering removed 93 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 8 clusters with 3 or more edges\n\nFiltering a set of 159 edges (7/8 clusters)                                                                                 \nFiltering a set of 159 edges (7/8 clusters). Pass 0, 560 triangles, 3 filtered edges\nFiltering a set of 156 edges (7/8 clusters). Pass 1, 214 triangles, 2 filtered edges\nFiltering a set of 154 edges (7/8 clusters). Pass 2, 192 triangles, 4 filtered edges\nFiltering a set of 150 edges (7/8 clusters). Pass 3, 181 triangles, 1 filtered edges\nFiltering a set of 149 edges (7/8 clusters). Pass 4, 175 triangles, 5 filtered edges\nFiltering a set of 144 edges (7/8 clusters). Pass 5, 165 triangles, 0 filtered edges\nFiltering a set of 387 edges (8/8 clusters)                                                                                 \nFiltering a set of 387 edges (8/8 clusters). Pass 0, 2967 triangles, 73 filtered edges\nFiltering a set of 314 edges (8/8 clusters). Pass 1, 102 triangles, 3 filtered edges\nFiltering a set of 311 edges (8/8 clusters). Pass 2, 96 triangles, 2 filtered edges\nFiltering a set of 309 edges (8/8 clusters). Pass 3, 92 triangles, 0 filtered edges\nEdge filtering identified 93 edges for removal\nEdge filtering removed 93 edges\nFitting the degree distribution to various densities\n"}