2026-06-08 10:15:08,577 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 10:15:15,568 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 10:15:15,569 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/fusion_contigs.ok

2026-06-08 10:15:15,570 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:15:15,573 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:15:15,573 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/cp_contigs_file_workdir

2026-06-08 10:15:15,575 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf

2026-06-08 10:15:15,577 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf

2026-06-08 10:15:15,577 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 10:15:15,579 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.I5K0LjK8JR/cytoBand.txt

2026-06-08 10:15:15,615 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.I5K0LjK8JR/cytoBand.txt

2026-06-08 10:15:15,615 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/cytoband.ok

2026-06-08 10:15:15,616 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed

2026-06-08 10:15:15,710 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed

2026-06-08 10:15:15,711 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 10:15:15,712 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:15:15,715 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:15:15,715 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok

2026-06-08 10:15:15,716 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:15:15,724 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:15:15,724 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok

2026-06-08 10:15:15,726 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz

2026-06-08 10:15:15,731 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz

2026-06-08 10:15:15,731 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok

2026-06-08 10:15:15,733 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:15:15,739 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:15:15,739 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/merged_contig_fai.ok

2026-06-08 10:15:15,740 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bUW-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.I5K0LjK8JR/fi_workdir --reads "/tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"

2026-06-08 11:26:39,423 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 71.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bUW-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.I5K0LjK8JR/fi_workdir --reads "/tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"

2026-06-08 11:26:39,423 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/run_STAR.ok

2026-06-08 11:26:39,426 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:26:42,916 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:26:42,916 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/mark_dup_reads.ok

2026-06-08 11:26:42,918 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 11:26:43,319 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 11:26:43,319 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 11:26:43,321 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:27:03,275 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:27:03,275 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 11:27:03,277 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:27:58,815 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:27:58,815 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 11:27:58,817 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary

2026-06-08 11:27:58,846 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary

2026-06-08 11:27:58,846 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 11:27:58,848 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:27:58,869 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:27:58,870 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 11:27:58,871 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:27:58,890 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:27:58,890 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 11:27:58,892 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:27:58,905 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:27:58,905 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 11:27:58,907 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"

2026-06-08 11:27:58,977 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"

2026-06-08 11:27:58,977 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 11:27:58,979 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam

2026-06-08 11:27:58,986 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam

2026-06-08 11:27:58,987 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 11:27:58,988 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed

2026-06-08 11:27:59,076 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed

2026-06-08 11:27:59,076 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok

2026-06-08 11:27:59,078 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,081 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,081 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok

2026-06-08 11:27:59,083 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,093 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,093 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok

2026-06-08 11:27:59,094 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:27:59,100 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:27:59,101 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok

2026-06-08 11:27:59,102 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:27:59,116 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:27:59,116 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/span_reads_acc.ok

2026-06-08 11:27:59,118 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:27:59,123 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:27:59,123 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 11:27:59,124 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : 

2026-06-08 11:27:59,160 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : 

2026-06-08 11:27:59,160 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_spanning_reads.ok

2026-06-08 11:27:59,162 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:27:59,166 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:27:59,166 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 11:27:59,168 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed

2026-06-08 11:27:59,183 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed

2026-06-08 11:27:59,183 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok

2026-06-08 11:27:59,185 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,186 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,187 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok

2026-06-08 11:27:59,188 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,193 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:27:59,193 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok

2026-06-08 11:27:59,194 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:27:59,199 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:27:59,199 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok

2026-06-08 11:27:59,201 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:27:59,209 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:27:59,209 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/cp_consol_bam.ok

2026-06-08 11:27:59,210 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:27:59,609 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:27:59,609 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/index_consol_bam.ok

2026-06-08 11:27:59,611 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:28:08,882 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:28:08,882 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 11:28:08,884 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan

2026-06-08 11:28:09,055 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan

2026-06-08 11:28:09,055 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 11:28:09,057 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 

2026-06-08 11:28:09,116 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 

2026-06-08 11:28:09,117 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 11:28:09,118 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed

2026-06-08 11:28:09,149 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed

2026-06-08 11:28:09,149 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 11:28:09,151 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 

2026-06-08 11:28:09,179 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 

2026-06-08 11:28:09,179 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 11:28:09,181 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed

2026-06-08 11:28:09,202 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed

2026-06-08 11:28:09,202 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 11:28:09,204 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:28:09,235 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:28:09,235 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/add_splice_info.ok

2026-06-08 11:28:09,237 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:28:09,382 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.I5K0LjK8JR/fi_workdir/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:28:09,383 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/blast_filter.ok

2026-06-08 11:28:09,384 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir

2026-06-08 11:28:09,402 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir

2026-06-08 11:28:09,402 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/annot_filter.ok

2026-06-08 11:28:09,404 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:28:09,425 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:28:09,425 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/EM_adj_counts.ok

2026-06-08 11:28:09,426 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:34:09,818 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 6.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:34:09,818 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/add_FFPM.ok

2026-06-08 11:34:09,821 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.I5K0LjK8JR/fi_workdir/microH.dat

2026-06-08 11:34:09,927 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.I5K0LjK8JR/fi_workdir/microH.dat

2026-06-08 11:34:09,927 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/microH.dat.ok

2026-06-08 11:34:09,929 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.I5K0LjK8JR/fi_workdir/microH.dat /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:34:09,958 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.I5K0LjK8JR/fi_workdir/microH.dat /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:34:09,958 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/append_microH_info.ok

2026-06-08 11:34:09,960 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv

2026-06-08 11:34:09,962 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv

2026-06-08 11:34:09,962 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/cp_final.ok

2026-06-08 11:34:09,964 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 11:34:09,978 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 11:34:09,978 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/final.abridged.ok

2026-06-08 11:34:09,980 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.I5K0LjK8JR --json_outfile /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bUW-T1-TRNA-1_B23WHTKLT4_1

2026-06-08 11:34:10,001 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.I5K0LjK8JR --json_outfile /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bUW-T1-TRNA-1_B23WHTKLT4_1

2026-06-08 11:34:10,001 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/create_fi_igvjs.ok

2026-06-08 11:34:10,003 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bUW-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html

2026-06-08 11:34:10,445 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bUW-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html

2026-06-08 11:34:10,445 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/fusion_reports_html.ok

2026-06-08 11:34:10,447 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:34:10,474 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:34:10,474 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/fusion_annotator.ok

2026-06-08 11:34:10,476 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.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:34:10,528 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.I5K0LjK8JR/ctat_genome_lib_build_dir > /tmp/nxf.I5K0LjK8JR/659_bUW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:34:10,528 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.I5K0LjK8JR/chckpts_dir/fusion_coding_region_effect.ok