diff --git a/CHANGELOG.md b/CHANGELOG.md
index d4d154029c47fe405fdc9aff2638a7d375cdb060..cb898370879238045e20bba88e38d1617dd41d69 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,8 +3,15 @@
 All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
+
+## [publish_1.0.6 ] - 2019-05-31
 ### Added
 - MIT LICENSE
+- Check for correct genome input
+- Check for correct output for motif serach
+
+### Fixed
+- Path to reference fasta file
 
 ## [publish_1.0.5 ] - 2019-05-16
 ### Fixed
diff --git a/LICENSE.md b/LICENSE.md
index aff8e3b4a3f5e77d9525a280d739f709477a54a5..5b4b67c8e0190980e6cdcaf7606476815b647c9b 100644
--- a/LICENSE.md
+++ b/LICENSE.md
@@ -4,7 +4,7 @@ Copyright (c) 2019, University of Texas Southwestern Medical Center.
 
 All rights reserved.
 
-Contributors: Spencer D. Barnes, Holly Ruess, Beibei Chen, Venkat S. Malladi
+Contributors: Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, Venkat S. Malladi
 
 Department: Bioinformatic Core Facility, Department of Bioinformatics
 
diff --git a/README.md b/README.md
index 99a5bd060bdddcb13603d487f34df85e52b2d3bd..39f934a388e6fd3e7e63ad65dd20efd5f05d6bb9 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # **CHIPseq Manual**
-## Version 1.0.5
-## May 16, 2019
+## Version 1.0.6
+## May 31, 2019
 
 # BICF ChIP-seq Pipeline
 
diff --git a/docs/references.md b/docs/references.md
index af633c8b4d7b8a19851ddaafd652e20f171d140c..c30998cc6a1ccc6e2f48c593b44cf066f49f7ff8 100644
--- a/docs/references.md
+++ b/docs/references.md
@@ -52,6 +52,6 @@
   * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
 
 17. **BICF ChIP-seq Analysis Workflow**:
-  * Spencer D. Barnes, Holly Ruess, Beibei Chen, & Venkat S. Malladi. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.5). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)
+  * Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, & Venkat S. Malladi. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.5). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)
 
 Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.
diff --git a/workflow/main.nf b/workflow/main.nf
index 2496d93ca2c9c82bcf996d0c854ac859c786ce18..9b45adb8235ef8964ac0d00fc86fd47b12d5cf0a 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -34,7 +34,7 @@ if (params.astrocyte) {
   referenceLocation = "/project/shared/bicf_workflow_ref"
   params.bwaIndex = "$referenceLocation/$params.genome"
   params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
-  params.fasta = "$referenceLocation/$params.genome/genome.fa.txt"
+  params.fasta = "$referenceLocation/$params.genome/genome.fa"
   if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
     params.genomeSize = 'hs'
   } else if (params.genome == 'GRCm38') {
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 79ea58ba8394a5b23e2600ee7472614fea861e1f..764106f7a529389e3de41f73b81600e0c37b92f8 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/workflow/scripts/annotate_peaks.R
@@ -1,10 +1,10 @@
 #!/bin/Rscript
 
-/*
- * --------------------------------------------------------------------------
- * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
- * --------------------------------------------------------------------------
- */
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+#* --------------------------------------------------------------------------
+#*
 
 # Load libraries
 library("ChIPseeker")
diff --git a/workflow/scripts/diff_peaks.R b/workflow/scripts/diff_peaks.R
index 2f567491fc83444d52eeb2bf30e3088a40913a10..3c5401e20b1c58235767f7c5a1e511c305c0a8db 100644
--- a/workflow/scripts/diff_peaks.R
+++ b/workflow/scripts/diff_peaks.R
@@ -1,10 +1,10 @@
 #!/bin/Rscript
 
-/*
- * --------------------------------------------------------------------------
- * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
- * --------------------------------------------------------------------------
- */
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
+#* --------------------------------------------------------------------------
+#*
 
 # Load libraries
 library("DiffBind")
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index a3a6abf85410682627095b02c995f34241387a31..9c09b0a9254ad0749cd36356212dd494b3162bf7 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -218,6 +218,13 @@ def main():
             shlex.split("samtools flagstat %s" % (bam_filename)),
             stdout=temp_file)
 
+    #Genome/Bad fastq File Check
+    file_check = open(bam_mapstats_filename).readlines()
+    percent = file_check[4].split('(')[1]
+    percent = percent.split('%')[0]
+    if float(percent) < 10:
+        raise Exception ('Mapped Genes too low: Check for correct Genotype')
+
     # Remove sai files
     for sai_file in sai:
         os.remove(sai_file)
diff --git a/workflow/tests/test_motif_search.py b/workflow/tests/test_motif_search.py
index 28aec0466d45ae1bf1185b5696b1c5fb669ef1c6..345c77ef0fe2c3f0009d83082b106e8eb039d3c2 100644
--- a/workflow/tests/test_motif_search.py
+++ b/workflow/tests/test_motif_search.py
@@ -21,7 +21,7 @@ def test_limited_peaks_singleend():
 def test_motif_search_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html'))
-
+    assert os.path.getsize(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa')) > 0
 
 @pytest.mark.singleskip_true
 def test_motif_search_singleend():
@@ -39,3 +39,4 @@ def test_limited_peaks_pairedend():
 def test_motif_search_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip',  'ENCSR729LGA.fa'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'index.html'))
+    assert os.path.getsize(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa')) > 0