Running on same CNV VCF file yields no results?

[johnemajor]

I am running truvari on a CNVnator generated VCF and specifying the same file as -b and -c, expecting too see perfect concordance. But instead truvari is reporting no matches at all? The CNVnator VCF entries look ok to me, ie:

Y 59363501 NA24385_CNVnator_del_2337 T . PASS END=59374000;SVTYPE=DEL;SVLEN=-10500;IMPRECISE;natorRD=0.00185287;natorP1=1.51783e-11;natorP2=2.76568e-212;natorP3=1.87497e-11;natorP4=1.57886e-183;natorQ0=0.999335 GT:CN 1/1:0

This is what the output log looks like

2019-11-23 11:27:03,931 [INFO] Running /home/ubuntu/conda/envs/wgspy3/bin/truvari -b ./NA24385.vcf.gz -c ./NA24385.vcf.gz -o Xxx -f /efs/WGS/data/reference/human/hum
an_g1k_v37_modified.fasta/human_g1k_v37_modified.fasta --sizemax 1000000
2019-11-23 11:27:03,931 [INFO] Params:
{
"pctovl": 0.0,
"sizemax": 1000000,
"includebed": null,
"sizefilt": 30,
"cSample": null,
"reference": "/efs/WGS/data/reference/human/human_g1k_v37_modified.fasta/human_g1k_v37_modified.fasta",
"no_ref": false,
"multimatch": false,
"comp": "./NA24385.vcf.gz",
"typeignore": false,
"refdist": 500,
"pctsize": 0.7,
"passonly": false,
"base": "./NA24385.vcf.gz",
"pctsim": 0.7,
"gtcomp": false,
"giabreport": false,
"debug": false,
"output": "Xxx",
"bSample": null,
"sizemin": 50
}
2019-11-23 11:27:03,944 [INFO] Creating call interval tree for overlap search
2019-11-23 11:27:04,122 [INFO] 2337 call variants
2019-11-23 11:27:04,122 [INFO] 2310 call variants within size range (30, 1000000)
2019-11-23 11:27:04,233 [INFO] 0 base variants
2019-11-23 11:27:04,291 [INFO] Matching base to calls
2019-11-23 11:27:04,405 [WARNING] No TP or FN calls in base!
2019-11-23 11:27:04,405 [INFO] Parsing FPs from calls
2019-11-23 11:27:04,616 [INFO] Stats: {
"FP": 0,
"f1": "NaN",
"base gt filtered": 0,
"precision": 0,
"TP-call": 0,
"call cnt": 0,
"base size filtered": 0,
"FN": 0,
"TP-base": 0,
"base cnt": 0,
"recall": 0,
"call gt filtered": 0,
"call size filtered": 0
}
2019-11-23 11:27:04,627 [INFO] Finished

[johnemajor]

This appears to be a problem with the conda install. When I created a fresh python3 ve with a new pip3 install as well, then installed truvari via pip, things work as expected.

[johnemajor]

.