INFO:root:{"type": "status update", "index": 0, "title": "Aligning", "status": 2, "msg": ""}
DEBUG:root:/opt/edge-filtering/edge/bin/bealign -q -r ./simulate/hiv.seq.ref.fasta -m HIV_BETWEEN_F -R data/seq_gen/C.Epidemic.fas /tmp/hivtrace-tiea445r/C.Epidemic.fas_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:/opt/edge-filtering/edge/bin/bam2msa /tmp/hivtrace-tiea445r/C.Epidemic.fas_output.bam /tmp/hivtrace-tiea445r/C.Epidemic.fas_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 -o /tmp/hivtrace-tiea445r/C.Epidemic.fas_user.tn93output.csv -t .03 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-tiea445r/C.Epidemic.fas_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:/opt/edge-filtering/edge/bin/hivnetworkcsv -i /tmp/hivtrace-tiea445r/C.Epidemic.fas_user.tn93output.csv -t .03 -f plain -j -o -n remove -s /tmp/hivtrace-tiea445r/C.Epidemic.fas_output.fasta
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 1 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 1 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 filtered edges\nFiltering a set of 38078 edges (1/1 clusters). Pass 5, 196608 triangles, 461 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 filtered edges\nFiltering a set of 38078 edges (1/1 clusters). Pass 5, 196608 triangles, 461 filtered edges\nFiltering a set of 37617 edges (1/1 clusters). Pass 6, 229376 triangles, 601 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 filtered edges\nFiltering a set of 38078 edges (1/1 clusters). Pass 5, 196608 triangles, 461 filtered edges\nFiltering a set of 37617 edges (1/1 clusters). Pass 6, 229376 triangles, 601 filtered edges\nFiltering a set of 37016 edges (1/1 clusters). Pass 7, 262144 triangles, 284 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 filtered edges\nFiltering a set of 38078 edges (1/1 clusters). Pass 5, 196608 triangles, 461 filtered edges\nFiltering a set of 37617 edges (1/1 clusters). Pass 6, 229376 triangles, 601 filtered edges\nFiltering a set of 37016 edges (1/1 clusters). Pass 7, 262144 triangles, 284 filtered edges\nEdge filtering identified 3539 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 filtered edges\nFiltering a set of 38078 edges (1/1 clusters). Pass 5, 196608 triangles, 461 filtered edges\nFiltering a set of 37617 edges (1/1 clusters). Pass 6, 229376 triangles, 601 filtered edges\nFiltering a set of 37016 edges (1/1 clusters). Pass 7, 262144 triangles, 284 filtered edges\nEdge filtering identified 3539 edges for removal\nEdge filtering removed 3539 edges\n"}
INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Running edge filtering on 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 filtered edges\nFiltering a set of 38078 edges (1/1 clusters). Pass 5, 196608 triangles, 461 filtered edges\nFiltering a set of 37617 edges (1/1 clusters). Pass 6, 229376 triangles, 601 filtered edges\nFiltering a set of 37016 edges (1/1 clusters). Pass 7, 262144 triangles, 284 filtered edges\nEdge filtering identified 3539 edges for removal\nEdge filtering removed 3539 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 1 clusters with 3 or more edges\n\nFiltering a set of 40271 edges (1/1 clusters)                                                                                 \nFiltering a set of 40271 edges (1/1 clusters). Pass 0, 32768 triangles, 44 filtered edges\nFiltering a set of 40227 edges (1/1 clusters). Pass 1, 65536 triangles, 679 filtered edges\nFiltering a set of 39548 edges (1/1 clusters). Pass 2, 98304 triangles, 686 filtered edges\nFiltering a set of 38862 edges (1/1 clusters). Pass 3, 131072 triangles, 331 filtered edges\nFiltering a set of 38531 edges (1/1 clusters). Pass 4, 163840 triangles, 453 filtered edges\nFiltering a set of 38078 edges (1/1 clusters). Pass 5, 196608 triangles, 461 filtered edges\nFiltering a set of 37617 edges (1/1 clusters). Pass 6, 229376 triangles, 601 filtered edges\nFiltering a set of 37016 edges (1/1 clusters). Pass 7, 262144 triangles, 284 filtered edges\nEdge filtering identified 3539 edges for removal\nEdge filtering removed 3539 edges\nFitting the degree distribution to various densities\n"}