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-0szjuq7p/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-0szjuq7p/C.Epidemic.fas_output.bam /tmp/hivtrace-0szjuq7p/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-0szjuq7p/C.Epidemic.fas_user.tn93output.csv -t .03 -a resolve -l 500 -g .05 -f csv /tmp/hivtrace-0szjuq7p/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-0szjuq7p/C.Epidemic.fas_user.tn93output.csv -t .03 -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"}