I am using JGIL on sequence data of fruit fly. Command as following:
./JGIL/jgil-1.6/jgil_m -M SRR1.bam SRR1.bam SRR3.bam -n 15 -f ref/D_simulans_ref.fasta -m 1 -o new_file
merge three bam files; inbreeding for 15 generation; using reference genome; output format as type 1; output prefix as "new_file" There is no error on the running log, but no output files!!
BAMs to be processed are merged.
Done parsing header text.
Doing SNP calling.
Number of generations for JGIL: 15
SNP quality threshold = 0 (this corresponds to a p-value of 1)
Mapping quality threshold = 0
Base quality threshold = 0
SNP output formats: tab
Prefix for output files = new_file
Reference sequence FASTA file(s): ref/D_simulans_ref.fasta
Running in unthreaded mode.
Processing 3 BAM files.
Processing reference: Scf_2L
Processing reference: Scf_2R
Processing reference: Scf_3L
Processing reference: Scf_3R
Processing reference: Scf_X
Reads considered = 19358407
Reads rejected - flagged unmapped 3
Reads rejected - low quality 0
Reads rejected - flagged multihit 0
Reads rejected - anomalous pair 0
Does anyone know there is the problem? Thanks very much!