Unknown Error

[rvrane]

Command Run- python3 scripts/DNAscan.py -format fastq -in /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R1_001.fastq -in2 /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R2_001.fastq -reference hg38 -alignment -variantcalling -annotation -out /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results/ -mode fast

ERROR-
############DNAscan Options############

DNAscan is running an anlysis with the following specifics:

format : fastq
rm_dup : True
BED : False
virus : False
input_file : /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R1_001.fastq
tmp : False
filter_string : QUAL > 1 & QUAL / INFO/AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1
input_file2 : /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/1-35197_GAGATTCC-AGGCTATA_L007_R2_001.fastq
mode : fast
out : /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results/
expansion : False
calls_report : False
alsgenescanner : False
annotation : True
iobio : False
results_report : False
paired : 1
dnascan_main_dir :
variantcalling : True
sample_name : sample
alignment : True
RG : False
vcf : None
sequencing_report : False
reference : hg38
alignment_report : False
exome : False
debug : False
SV : False
bacteria : False
ref_file :
custom_microbes : False

Options saved onto /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results///logs/options.log

/tmp
samblaster: Version 0.1.26
samblaster: Inputting from stdin
samblaster: Outputting to stdout

sambamba 0.7.1
by Artem Tarasov and Pjotr Prins (C) 2012-2019
LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)

(ERR): "/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/DNAscan/hg19/hg19" does not exist
Exiting now ...
samblaster: Input file is empty. Exiting.
samblaster: Premature exit (return code 1).
Tue 28 Jul 16:52:36 BST 2020
Error: Failed to set region: -1:0-249,250,621()
ERROR(freebayes): Could not SetRegion to chr1:0..249250621
Error: Failed to set region: -1:0-243,199,373()
ERROR(freebayes): Could not SetRegion to chr2:0..243199373
Error: Failed to set region: -1:0-198,022,430()
ERROR(freebayes): Could not SetRegion to chr3:0..198022430
Error: Failed to set region: -1:0-191,154,276()
ERROR(freebayes): Could not SetRegion to chr4:0..191154276
Error: Failed to set region: -1:0-180,915,260()
ERROR(freebayes): Could not SetRegion to chr5:0..180915260
Error: Failed to set region: -1:0-171,115,067()
ERROR(freebayes): Could not SetRegion to chr6:0..171115067
Error: Failed to set region: -1:0-159,138,663()
ERROR(freebayes): Could not SetRegion to chr7:0..159138663
Error: Failed to set region: -1:0-146,364,022()
ERROR(freebayes): Could not SetRegion to chr8:0..146364022
Error: Failed to set region: -1:0-141,213,431()
ERROR(freebayes): Could not SetRegion to chr9:0..141213431
Error: Failed to set region: -1:0-135,534,747()
ERROR(freebayes): Could not SetRegion to chr10:0..135534747
Error: Failed to set region: -1:0-135,006,516()
ERROR(freebayes): Could not SetRegion to chr11:0..135006516
Error: Failed to set region: -1:0-133,851,895()
ERROR(freebayes): Could not SetRegion to chr12:0..133851895
Error: Failed to set region: -1:0-115,169,878()
ERROR(freebayes): Could not SetRegion to chr13:0..115169878
Error: Failed to set region: -1:0-107,349,540()
ERROR(freebayes): Could not SetRegion to chr14:0..107349540
Error: Failed to set region: -1:0-102,531,392()
ERROR(freebayes): Could not SetRegion to chr15:0..102531392
Error: Failed to set region: -1:0-90,354,753()
ERROR(freebayes): Could not SetRegion to chr16:0..90354753
Error: Failed to set region: -1:0-81,195,210()
ERROR(freebayes): Could not SetRegion to chr17:0..81195210
Error: Failed to set region: -1:0-78,077,248()
ERROR(freebayes): Could not SetRegion to chr18:0..78077248
Error: Failed to set region: -1:0-59,128,983()
ERROR(freebayes): Could not SetRegion to chr19:0..59128983
Error: Failed to set region: -1:0-63,025,520()
ERROR(freebayes): Could not SetRegion to chr20:0..63025520
Error: Failed to set region: -1:0-48,129,895()
ERROR(freebayes): Could not SetRegion to chr21:0..48129895
Error: Failed to set region: -1:0-51,304,566()
ERROR(freebayes): Could not SetRegion to chr22:0..51304566
Error: Failed to set region: -1:0-59,373,566()
ERROR(freebayes): Could not SetRegion to chrY:0..59373566
Error: Failed to set region: -1:0-155,270,560()
ERROR(freebayes): Could not SetRegion to chrX:0..155270560
Error: Failed to set region: -1:0-16,571(*)
ERROR(freebayes): Could not SetRegion to chrM:0..16571
Tue 28 Jul 16:53:27 BST 2020
/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane//Miniconda2/bin/bcftools filter -i " QUAL > 1 & QUAL / INFO/AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1 " /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//sample_sorted.vcf.gz | bgzip -c > /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//sample_sorted_filtered.vcf.gz ; /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane//Miniconda2/bin/tabix -fp vcf /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//sample_sorted_filtered.vcf.gz
NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)
Error: the required database file /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/humandb/hg38_refGene.txt does not exist.
rm: cannot remove '/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//annovar.vcf.hg19_multianno.txt': No such file or directory
rm: cannot remove '/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//annovar.vcf.avinput': No such file or directory
mv: cannot stat '/home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results///annovar.vcf.hg19_multianno.vcf': No such file or directory
[bgzip] No such file or directory: /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//results/sample_annotated.vcf
tbx_index_build failed: /home/wubuntu/Desktop/xfr_dtd-260/rugved_rane/PilotRaw/Raw/Sample_1-35197/SEQ/results//results/sample_annotated.vcf.gz

I am trying to use the pipeline locally.
After following all the mentioned steps, i tried running the example files and the same error occured.

I can see the output directory being created with no reports or result files.
Can you please help me identify this problem and fix it since i want to use this pipeline to run HLA region genomic data.