genome index is regenerated even if it already exists

[bounlu]

gemBS index command regenerates the genome index even though it already exists as prepared in advance. It overwrites the existing file genome.gemBS.gem in the below settings.

The documentation says:

# Note that the index and contig_sizes files are generated from the
# reference file if they do not already exist

So I would expect the indexing would be skipped in my case. The rest of the commands gemBS map etc. work fine after the index is regenerated.

I am wondering what I am doing wrong or whether this is a bug?

My commands:

gemBS prepare -c gembsrs.config -t input.txt
gemBS index

My gembsrs.config file:

base = "/home"

index_dir = ${base}/reference
sequence_dir = ${base}/fastq
bam_dir = ${base}/mapping
bcf_dir = ${base}/calling
extract_dir = ${base}/extract
report_dir = ${base}/report

# hg38 genome index prepared in advance
reference = ${base}/reference/genome.fasta
index = ${base}/reference/genome.gemBS.gem

jobs = 8
cores = 32
threads = 64
memory = 256G


[dbsnp]

# dbsnp index prepared in advance
dbsnp_files = ${base}/reference/dbsnp_146.hg38.vcf.gz
dbsnp_index = ${base}/reference/dbsnp_146.hg38.gemBS.vcf.idx
dbsnp_type = "VCF"

[mapping]

non_stranded = False
remove_individual_bams = True

[calling]

jobs = 8
mapq_threshold = 10
qual_threshold = 13
reference_bias = 2
left_trim = 5
right_trim = 0
keep_improper_pairs = False
keep_duplicates = False
haploid = False
conversion = 0.01,0.05
remove_individual_bcfs = True
contig_pool_limit = 25000000

[extract]

jobs = 8
strand_specific = True
bigwig_strand_specific = True
phred_threshold = 10
make_cpg = True
make_non_cpg = True
make_bedmethyl = True
make_bigwig = True
make_snps = True

Log:

INFO - Launch:
	/usr/local/lib/gemBS/bin/gem-indexer -i ./reference/genome.gemBS.ref -o ./reference/genome.gemBS --bisulfite-index --threads 64 --tmp-folder ./reference