Open bounlu opened 2 years ago
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.
gemBS index
genome.gemBS.gem
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.
gemBS map
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:
gembsrs.config
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
gemBS index
command regenerates the genome index even though it already exists as prepared in advance. It overwrites the existing filegenome.gemBS.gem
in the below settings.The documentation says:
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:
My
gembsrs.config
file:Log: