caper halted

[zji90]

I am running caper on a very large bam file (96G). It halted when running atac.fraglen_stat_pe and the log shows it's calculating jsd. However, I do not see any cromwell instance running (previously there was one running). I wonder if the whole program is still running or there is anything wrong?

Code to call caper:
caper hpc submit atac.wdl -i input.json --singularity --leader-job-name a

input.json:
{
"atac.pipeline_type" : "atac",
"atac.genome_tsv" : "/hpc/group/jilab/zj/encode/encfile/hg38/hg38.tsv",
"atac.nodup_bams" : ["/hpc/group/jilab/zj/encode/splitbam/level2/level2-Homo_sapiens-heart_left_ventricle-cardiomyocyte-male-adult_child.bam"],
"atac.paired_end" : true,
"atac.auto_detect_adapter" : true,
"atac.ref_fa" : "/hpc/group/jilab/zj/encode/encfile/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz",
"atac.blacklist" : "/hpc/group/jilab/zj/encode/encfile/hg38/ENCFF356LFX.bed.gz",
"atac.prom" : "/hpc/group/jilab/zj/encode/encfile/hg38/ENCFF140XLU.bed.gz",
"atac.dnase" : "/hpc/group/jilab/zj/encode/encfile/hg38/ENCFF304XEX.bed.gz",
"atac.enh" : "/hpc/group/jilab/zj/encode/encfile/hg38/ENCFF212UAV.bed.gz",
"atac.tss" : "/hpc/group/jilab/zj/encode/encfile/hg38/ENCFF766FGL.bed.gz",
"atac.chrsz" : "/hpc/group/jilab/zj/encode/encfile/hg38/GRCh38_EBV.chrom.sizes.tsv"
}