FusionInspector.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (HD789_0002_RNA_0008_23H5VFLT4_s19)

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/d2a197f3f475af9955c243b3506580/FusionInspector.log
Size: 43.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (HD789_0002_RNA_0008_23H5VFLT4_s19)
Attempt
Content

2026-06-08 10:00:59,119 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions HD789_0002_RNA_0008_23H5VFLT4_s19.fusionreport.tsv --gtf /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19 --shrink_introns --max_intron_length 1000 

2026-06-08 10:01:06,910 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions HD789_0002_RNA_0008_23H5VFLT4_s19.fusionreport.tsv --gtf /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19 --shrink_introns --max_intron_length 1000 

2026-06-08 10:01:06,910 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/fusion_contigs.ok

2026-06-08 10:01:06,911 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fa

2026-06-08 10:01:06,915 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fa

2026-06-08 10:01:06,915 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/cp_contigs_file_workdir

2026-06-08 10:01:06,917 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf

2026-06-08 10:01:06,922 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf

2026-06-08 10:01:06,922 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 10:01:06,924 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf > /tmp/nxf.lZyWkWKT6L/cytoBand.txt

2026-06-08 10:01:07,054 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf > /tmp/nxf.lZyWkWKT6L/cytoBand.txt

2026-06-08 10:01:07,054 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/cytoband.ok

2026-06-08 10:01:07,056 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed

2026-06-08 10:01:07,430 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed

2026-06-08 10:01:07,430 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 10:01:07,432 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.sorted.bed

2026-06-08 10:01:07,435 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.sorted.bed

2026-06-08 10:01:07,435 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.bedsort.ok

2026-06-08 10:01:07,436 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.sorted.bed

2026-06-08 10:01:07,450 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.sorted.bed

2026-06-08 10:01:07,450 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.bgzip.ok

2026-06-08 10:01:07,452 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.sorted.bed.gz

2026-06-08 10:01:07,459 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.sorted.bed.gz

2026-06-08 10:01:07,460 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.bed.tabix.ok

2026-06-08 10:01:07,461 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa

2026-06-08 10:01:07,473 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa

2026-06-08 10:01:07,473 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/merged_contig_fai.ok

2026-06-08 10:01:07,475 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fa --max_mate_dist 100000 -G /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf --CPU 8 --out_prefix HD789_0002_RNA_0008_23H5VFLT4_s19.star --out_dir /tmp/nxf.lZyWkWKT6L/fi_workdir --reads "/tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19_1.fastp.fastq.gz /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19_2.fastp.fastq.gz"

2026-06-08 11:03:13,110 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 62.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fa --max_mate_dist 100000 -G /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf --CPU 8 --out_prefix HD789_0002_RNA_0008_23H5VFLT4_s19.star --out_dir /tmp/nxf.lZyWkWKT6L/fi_workdir --reads "/tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19_1.fastp.fastq.gz /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19_2.fastp.fastq.gz"

2026-06-08 11:03:13,110 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/run_STAR.ok

2026-06-08 11:03:13,113 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.sortedByCoord.out.bam   -o /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:03:44,575 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.sortedByCoord.out.bam   -o /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:03:44,575 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/mark_dup_reads.ok

2026-06-08 11:03:44,577 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam

2026-06-08 11:03:48,251 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam

2026-06-08 11:03:48,251 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 11:03:48,254 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:06:55,587 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 3.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:06:55,587 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 11:06:55,590 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:16:03,168 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 9.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:16:03,169 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 11:16:03,171 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary

2026-06-08 11:16:03,613 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary

2026-06-08 11:16:03,613 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 11:16:03,615 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:16:04,057 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:16:04,057 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 11:16:04,059 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:16:04,100 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:16:04,100 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 11:16:04,102 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:16:04,133 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:16:04,134 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 11:16:04,135 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam"

2026-06-08 11:16:04,284 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam"

2026-06-08 11:16:04,284 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 11:16:04,286 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam

2026-06-08 11:16:04,303 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam

2026-06-08 11:16:04,304 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 11:16:04,305 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed

2026-06-08 11:16:04,635 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed

2026-06-08 11:16:04,635 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bam_to_bed.ok

2026-06-08 11:16:04,637 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,647 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,647 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bedsort.ok

2026-06-08 11:16:04,649 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,675 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,675 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bgzip.ok

2026-06-08 11:16:04,677 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:16:04,687 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:16:04,687 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.junction_reads.bam.tabix.ok

2026-06-08 11:16:04,689 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:16:04,719 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:16:04,719 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/span_reads_acc.ok

2026-06-08 11:16:04,721 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam

2026-06-08 11:16:04,727 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam

2026-06-08 11:16:04,727 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 11:16:04,729 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam || : 

2026-06-08 11:16:04,779 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa -  | samtools sort -@ 8 - -o /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam || : 

2026-06-08 11:16:04,779 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_spanning_reads.ok

2026-06-08 11:16:04,781 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam

2026-06-08 11:16:04,786 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam

2026-06-08 11:16:04,786 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 11:16:04,788 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed

2026-06-08 11:16:04,812 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed

2026-06-08 11:16:04,812 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bam_to_bed.ok

2026-06-08 11:16:04,814 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,816 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,816 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bedsort.ok

2026-06-08 11:16:04,817 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,823 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:16:04,823 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bgzip.ok

2026-06-08 11:16:04,824 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:16:04,830 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:16:04,830 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/HD789_0002_RNA_0008_23H5VFLT4_s19.spanning_reads.bam.tabix.ok

2026-06-08 11:16:04,832 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam

2026-06-08 11:16:04,884 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.star.cSorted.dupsMarked.bam /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam

2026-06-08 11:16:04,884 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/cp_consol_bam.ok

2026-06-08 11:16:04,886 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam

2026-06-08 11:16:08,544 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam

2026-06-08 11:16:08,544 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/index_consol_bam.ok

2026-06-08 11:16:08,546 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:17:32,750 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 1.40 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:17:32,750 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 11:17:32,752 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam.frag_coords > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.FusionJuncSpan

2026-06-08 11:17:34,126 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.consolidated.bam.frag_coords > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.FusionJuncSpan

2026-06-08 11:17:34,126 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 11:17:34,128 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.Pfam.gff3 

2026-06-08 11:17:34,359 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.Pfam.gff3 

2026-06-08 11:17:34,359 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 11:17:34,361 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.Pfam.gff3 > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.Pfam.bed

2026-06-08 11:17:34,462 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.Pfam.gff3 > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.Pfam.bed

2026-06-08 11:17:34,463 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 11:17:34,464 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.seqsimilar.gff3 

2026-06-08 11:17:34,526 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.seqsimilar.gff3 

2026-06-08 11:17:34,526 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 11:17:34,528 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.seqsimilar.gff3 > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.seqsimilar.bed

2026-06-08 11:17:34,549 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.seqsimilar.gff3 > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.igv.seqsimilar.bed

2026-06-08 11:17:34,549 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 11:17:34,551 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:17:34,658 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa > /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:17:34,658 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/add_splice_info.ok

2026-06-08 11:17:34,660 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:17:34,848 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.lZyWkWKT6L/fi_workdir/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:17:34,848 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/blast_filter.ok

2026-06-08 11:17:34,850 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir

2026-06-08 11:17:34,880 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir

2026-06-08 11:17:34,880 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/annot_filter.ok

2026-06-08 11:17:34,882 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:17:34,940 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:17:34,940 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/EM_adj_counts.ok

2026-06-08 11:17:34,942 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19_1.fastp.fastq.gz /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:23:38,924 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 6.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19_1.fastp.fastq.gz /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:23:38,924 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/add_FFPM.ok

2026-06-08 11:23:38,926 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa --gtf /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf  > /tmp/nxf.lZyWkWKT6L/fi_workdir/microH.dat

2026-06-08 11:23:39,401 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fa --gtf /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.gtf  > /tmp/nxf.lZyWkWKT6L/fi_workdir/microH.dat

2026-06-08 11:23:39,401 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/microH.dat.ok

2026-06-08 11:23:39,403 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.lZyWkWKT6L/fi_workdir/microH.dat /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:23:39,586 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.lZyWkWKT6L/fi_workdir/microH.dat /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:23:39,586 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/append_microH_info.ok

2026-06-08 11:23:39,588 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.tsv

2026-06-08 11:23:39,593 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.tsv

2026-06-08 11:23:39,593 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/cp_final.ok

2026-06-08 11:23:39,594 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv

2026-06-08 11:23:39,614 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv

2026-06-08 11:23:39,614 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/final.abridged.ok

2026-06-08 11:23:39,616 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lZyWkWKT6L --json_outfile /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_inspector_web.json --file_prefix HD789_0002_RNA_0008_23H5VFLT4_s19

2026-06-08 11:23:39,636 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lZyWkWKT6L --json_outfile /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_inspector_web.json --file_prefix HD789_0002_RNA_0008_23H5VFLT4_s19

2026-06-08 11:23:39,637 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/create_fi_igvjs.ok

2026-06-08 11:23:39,638 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_inspector_web.json --input_file_prefix HD789_0002_RNA_0008_23H5VFLT4_s19 --html_output /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_inspector_web.html

2026-06-08 11:23:41,400 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_inspector_web.json --input_file_prefix HD789_0002_RNA_0008_23H5VFLT4_s19 --html_output /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.fusion_inspector_web.html

2026-06-08 11:23:41,400 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/fusion_reports_html.ok

2026-06-08 11:23:41,402 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:23:41,439 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:23:41,439 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/fusion_annotator.ok

2026-06-08 11:23:41,441 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:23:41,778 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.lZyWkWKT6L/ctat_genome_lib_build_dir > /tmp/nxf.lZyWkWKT6L/HD789_0002_RNA_0008_23H5VFLT4_s19.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:23:41,779 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.lZyWkWKT6L/chckpts_dir/fusion_coding_region_effect.ok