INFO:root:{"type": "status update", "index": 0, "title": "Aligning", "status": 2, "msg": ""} DEBUG:root:/home/sweaver/programming/hivtrace/edge/bin/bealign -q -r HXB2_prrt -m HIV_BETWEEN_F -R data/sim_seq/8_0_0.01_0.19_sim.fasta /tmp/hivtrace-1_rrql4d/8_0_0.01_0.19_sim.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/edge/bin/bam2msa /tmp/hivtrace-1_rrql4d/8_0_0.01_0.19_sim.fasta_output.bam /tmp/hivtrace-1_rrql4d/8_0_0.01_0.19_sim.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 -o /tmp/hivtrace-1_rrql4d/8_0_0.01_0.19_sim.fasta_user.tn93output.csv -t .015 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-1_rrql4d/8_0_0.01_0.19_sim.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/edge/bin/hivnetworkcsv -i /tmp/hivtrace-1_rrql4d/8_0_0.01_0.19_sim.fasta_user.tn93output.csv -t .015 -f plain -j -o INFO:root:{"type": "status update", "index": 4, "title": "Inferring, filtering, and analyzing molecular transmission network", "status": 2, "msg": "Fitting 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": "Fitting the degree distribution to various densities\n"}