diff --git a/Snakefile b/Snakefile
index 80e371b7c8dd35d22916ae20aeabee6cafe388f0..9ca01cacd37be6bbc0ff41c978ce92ab67794eed 100644
--- a/Snakefile
+++ b/Snakefile
@@ -705,7 +705,7 @@ rule create_haplotag_table:
     output:
         tsv='haplotag/table/{sample}/by-cell/haplotag-counts.{cell}.{windows}.{bpdens}.tsv'
     log:
-        "log/create_haplotag_table/{sample}.{cell}.log"
+        "log/create_haplotag_table/{sample}.{cell}.{windows}.{bpdens}.log"
     script:
         "utils/haplotagTable.snakemake.R"
 
@@ -720,11 +720,11 @@ rule merge_haplotag_tables:
 
 rule create_haplotag_likelihoods:
     input:
-        haplotag_table='haplotag/table/{sample}/haplotag-counts.{windows}.{bpdens}.tsv'
-        sv_probs_table = 'sv_probabilities/{sample}/{windows}.{bpdens}/probabilities.Rdata'
+        haplotag_table='haplotag/table/{sample}/full/haplotag-counts.{windows}.{bpdens}.tsv',
+        sv_probs_table = 'sv_probabilities/{sample}/{windows}.{bpdens}/probabilities.Rdata',
     output: 'haplotag/table/{sample}/haplotag-likelihoods.{windows}.{bpdens}.data'
     log:
-        "log/create_haplotag_likelihoods/{sample}.log"
+        "log/create_haplotag_likelihoods/{sample}.{windows}.{bpdens}.log"
     script:
         "utils/haplotagProbs.snakemake.R"
 
diff --git a/utils/haplotagProbs.snakemake.R b/utils/haplotagProbs.snakemake.R
index 14e14dffc6c5fe2e8b9cc714ca6d30c78e45c7f3..2518e6ffd9d1dd4150aa397d8b6bc39548af752d 100644
--- a/utils/haplotagProbs.snakemake.R
+++ b/utils/haplotagProbs.snakemake.R
@@ -1,8 +1,12 @@
-sink(snakemake@log[[1]])
+log <- file(snakemake@log[[1]], open='wt')
+sink(file=log, type='message')
+sink(file=log, type='output')
 
-haplotagCounts <- snakemake@input[[haplotag_table]]
-probs <- snakemake@input[[sv_probs_table]]
+source('utils/haplotagProbs.R')
 
-probs <- addHaploCountProbs(probs, haploCounts, alpha)
+haplotagCounts <- fread(snakemake@input[["haplotag_table"]])
+probs <- readRDS(snakemake@input[["sv_probs_table"]])
 
-save(probs, file=snakemake@output[[1]])
\ No newline at end of file
+probs <- addHaploCountProbs(probs, haplotagCounts, alpha=0.05)
+
+saveRDS(probs, file=snakemake@output[[1]])