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!!

log:

BAMs to be processed are merged.

Done parsing header text.

Sample names:

JGIL v1.6

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!