2026-06-08 10:05:31,420 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 10:05:38,446 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_bGW-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 10:05:38,446 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/fusion_contigs.ok

2026-06-08 10:05:38,448 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:05:38,450 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:05:38,450 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/cp_contigs_file_workdir

2026-06-08 10:05:38,451 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf

2026-06-08 10:05:38,455 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf

2026-06-08 10:05:38,455 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 10:05:38,457 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.3HaMgINLT2/cytoBand.txt

2026-06-08 10:05:38,509 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.3HaMgINLT2/cytoBand.txt

2026-06-08 10:05:38,509 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/cytoband.ok

2026-06-08 10:05:38,511 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed

2026-06-08 10:05:38,680 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed

2026-06-08 10:05:38,680 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 10:05:38,682 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:05:38,684 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:05:38,684 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok

2026-06-08 10:05:38,685 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:05:38,695 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 10:05:38,695 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok

2026-06-08 10:05:38,696 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz

2026-06-08 10:05:38,702 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz

2026-06-08 10:05:38,702 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok

2026-06-08 10:05:38,704 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:05:38,710 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 10:05:38,710 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/merged_contig_fai.ok

2026-06-08 10:05:38,712 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.3HaMgINLT2/fi_workdir --reads "/tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"

2026-06-08 11:19:06,171 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 73.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.3HaMgINLT2/fi_workdir --reads "/tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"

2026-06-08 11:19:06,171 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/run_STAR.ok

2026-06-08 11:19:06,174 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:19:15,198 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:19:15,198 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/mark_dup_reads.ok

2026-06-08 11:19:15,200 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 11:19:16,250 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 11:19:16,250 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 11:19:16,252 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:20:12,710 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.94 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:20:12,710 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 11:20:12,712 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:23:05,038 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 2.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:23:05,039 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 11:23:05,041 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary

2026-06-08 11:23:05,067 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary

2026-06-08 11:23:05,067 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 11:23:05,068 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:23:05,087 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:23:05,087 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 11:23:05,089 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:23:05,107 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:23:05,107 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 11:23:05,109 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:23:05,122 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:23:05,122 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 11:23:05,124 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"

2026-06-08 11:23:05,190 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"

2026-06-08 11:23:05,190 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 11:23:05,192 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam

2026-06-08 11:23:05,198 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam

2026-06-08 11:23:05,198 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 11:23:05,200 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed

2026-06-08 11:23:05,266 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed

2026-06-08 11:23:05,266 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok

2026-06-08 11:23:05,268 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,271 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,271 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok

2026-06-08 11:23:05,272 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,280 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,280 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok

2026-06-08 11:23:05,282 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:23:05,288 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:23:05,288 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok

2026-06-08 11:23:05,290 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:23:05,303 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:23:05,303 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/span_reads_acc.ok

2026-06-08 11:23:05,304 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:23:05,309 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:23:05,309 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 11:23:05,311 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : 

2026-06-08 11:23:05,347 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : 

2026-06-08 11:23:05,348 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_spanning_reads.ok

2026-06-08 11:23:05,349 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:23:05,354 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 11:23:05,354 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 11:23:05,356 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed

2026-06-08 11:23:05,371 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed

2026-06-08 11:23:05,371 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok

2026-06-08 11:23:05,372 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,374 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,374 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok

2026-06-08 11:23:05,375 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,380 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:23:05,380 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok

2026-06-08 11:23:05,381 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:23:05,386 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:23:05,386 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok

2026-06-08 11:23:05,387 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:23:05,403 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:23:05,403 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/cp_consol_bam.ok

2026-06-08 11:23:05,405 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:23:06,452 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 11:23:06,452 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/index_consol_bam.ok

2026-06-08 11:23:06,454 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:23:33,660 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:23:33,661 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 11:23:33,663 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan

2026-06-08 11:23:34,152 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan

2026-06-08 11:23:34,152 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 11:23:34,154 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 

2026-06-08 11:23:34,239 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 

2026-06-08 11:23:34,239 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 11:23:34,241 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed

2026-06-08 11:23:34,277 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed

2026-06-08 11:23:34,277 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 11:23:34,279 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 

2026-06-08 11:23:34,315 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 

2026-06-08 11:23:34,315 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 11:23:34,317 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed

2026-06-08 11:23:34,337 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed

2026-06-08 11:23:34,337 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 11:23:34,339 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:23:34,378 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:23:34,378 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/add_splice_info.ok

2026-06-08 11:23:34,380 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:23:34,523 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.3HaMgINLT2/fi_workdir/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:23:34,523 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/blast_filter.ok

2026-06-08 11:23:34,525 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir

2026-06-08 11:23:34,543 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir

2026-06-08 11:23:34,543 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/annot_filter.ok

2026-06-08 11:23:34,545 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:23:34,562 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:23:34,562 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/EM_adj_counts.ok

2026-06-08 11:23:34,564 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:29:23,224 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:29:23,224 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/add_FFPM.ok

2026-06-08 11:29:23,226 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.3HaMgINLT2/fi_workdir/microH.dat

2026-06-08 11:29:23,369 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.3HaMgINLT2/fi_workdir/microH.dat

2026-06-08 11:29:23,369 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/microH.dat.ok

2026-06-08 11:29:23,371 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.3HaMgINLT2/fi_workdir/microH.dat /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:29:23,397 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.3HaMgINLT2/fi_workdir/microH.dat /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:29:23,397 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/append_microH_info.ok

2026-06-08 11:29:23,399 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv

2026-06-08 11:29:23,401 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv

2026-06-08 11:29:23,401 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/cp_final.ok

2026-06-08 11:29:23,403 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 11:29:23,416 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 11:29:23,416 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/final.abridged.ok

2026-06-08 11:29:23,418 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.3HaMgINLT2 --json_outfile /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1

2026-06-08 11:29:23,438 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.3HaMgINLT2 --json_outfile /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1

2026-06-08 11:29:23,438 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/create_fi_igvjs.ok

2026-06-08 11:29:23,440 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html

2026-06-08 11:29:24,021 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html

2026-06-08 11:29:24,021 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/fusion_reports_html.ok

2026-06-08 11:29:24,023 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:29:24,046 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:29:24,046 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/fusion_annotator.ok

2026-06-08 11:29:24,047 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:29:24,186 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.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.3HaMgINLT2/ctat_genome_lib_build_dir > /tmp/nxf.3HaMgINLT2/659_bGW-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:29:24,186 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.3HaMgINLT2/chckpts_dir/fusion_coding_region_effect.ok