Why do I get an empty output file?

[lichangyaya]

Hello，
My input file is GRCh37 human gene and virus gene, why can't I get the output file.
The configuration file is as follows:
snakedir: "/home/lc/isling"
global:
out_dir: "out/GRCh37_test15"
read information
read_folder: "test/reads/"
R1_suffix: "_001.fastq"
R2_suffix: "_002.fastq"
read1-adapt: "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"
read2-adapt: "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
split: 3
mean-frag-len: "estimate"
read preprocessing options
dedup: True
merge: True
trim: True
dedup-subs: 2
alignment options
host_name: "GRCh37"
host_fasta: "test/references/GRCh37.fa"
virus_name: "10791"
virus_fasta: "test/references/10791.fa"
bwa-mem: "-a -t 4 -k 15 -W 25 -r 1.0 -A 1 -B 3 -O 5,5 -E 1,1 -L 0 -U 15 -T 0"
align-cpus: 4
integration detection options
clip-cutoff: 20
cigar-tol: 3
alt-edit-dist-thresh: 2
alt-edit-dist-thresh-pc: 0.6
filter:

• "HostEditDist <= 5"
• "ViralEditDist <= 5"
• "NoAmbiguousBases < 20 or Type == discordant"
• "PossibleVectorRearrangement == False"
• "PossibleHostTranslocation == False"
  bed-exclude:
• test/references/test.bed
  merge-method: 'common'
  merge-n-min: 1
  mapq-threshold: 20
  test-merge:
  merge: True

[szsctt]

Are all the output files in the out/GRCh37_test15/ints empty? If isling ran without any errors (snakemake will report failed jobs), then the most likely explanation is that your data doesn't contain integration sites.