2026-06-04 22:11:59,627 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_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 

2026-06-04 22:12:12,536 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 

2026-06-04 22:12:12,536 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/fusion_contigs.ok

2026-06-04 22:12:12,539 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:12:12,543 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:12:12,553 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/cp_contigs_file_workdir

2026-06-04 22:12:12,555 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf

2026-06-04 22:12:12,563 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf

2026-06-04 22:12:12,563 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-04 22:12:12,566 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.xUJ2ieXBIN/cytoBand.txt

2026-06-04 22:12:12,700 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.xUJ2ieXBIN/cytoBand.txt

2026-06-04 22:12:12,700 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/cytoband.ok

2026-06-04 22:12:12,703 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed

2026-06-04 22:12:12,978 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed

2026-06-04 22:12:12,979 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-04 22:12:12,982 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:12:12,985 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:12:12,986 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok

2026-06-04 22:12:12,988 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:12:13,013 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:12:13,013 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok

2026-06-04 22:12:13,016 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz

2026-06-04 22:12:13,027 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz

2026-06-04 22:12:13,027 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok

2026-06-04 22:12:13,030 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:12:13,055 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:12:13,056 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/merged_contig_fai.ok

2026-06-04 22:12:13,059 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.xUJ2ieXBIN/fi_workdir --reads "/tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"

2026-06-04 23:39:57,234 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 87.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.xUJ2ieXBIN/fi_workdir --reads "/tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"

2026-06-04 23:39:57,235 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/run_STAR.ok

2026-06-04 23:39:57,237 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-04 23:40:08,233 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-04 23:40:08,233 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/mark_dup_reads.ok

2026-06-04 23:40:08,236 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

2026-06-04 23:40:09,597 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

2026-06-04 23:40:09,597 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/mark_dups_reads.index.ok

2026-06-04 23:40:09,600 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-04 23:41:19,575 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 1.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-04 23:41:19,575 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-04 23:41:19,578 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-04 23:44:46,833 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 3.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-04 23:44:46,833 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-04 23:44:46,836 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary

2026-06-04 23:44:46,873 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary

2026-06-04 23:44:46,873 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/coalesce_junc_n_span.ok

2026-06-04 23:44:46,876 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-04 23:44:46,912 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-04 23:44:46,912 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/init_EM_adj_counts.ok

2026-06-04 23:44:46,915 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-04 23:44:46,934 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-04 23:44:46,934 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/filter_by_frag_threshs.ok

2026-06-04 23:44:46,937 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-04 23:44:46,952 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-04 23:44:46,952 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-04 23:44:46,955 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"

2026-06-04 23:44:47,039 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"

2026-06-04 23:44:47,039 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-04 23:44:47,042 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam

2026-06-04 23:44:47,054 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam

2026-06-04 23:44:47,054 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-04 23:44:47,056 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed

2026-06-04 23:44:47,165 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed

2026-06-04 23:44:47,165 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok

2026-06-04 23:44:47,167 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,171 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,172 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok

2026-06-04 23:44:47,174 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,186 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,186 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok

2026-06-04 23:44:47,188 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,196 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,196 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok

2026-06-04 23:44:47,198 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-04 23:44:47,214 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-04 23:44:47,214 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/span_reads_acc.ok

2026-06-04 23:44:47,216 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,223 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,223 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/init_spanning_reads_bam.ok

2026-06-04 23:44:47,226 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 

2026-06-04 23:44:47,266 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 

2026-06-04 23:44:47,267 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_spanning_reads.ok

2026-06-04 23:44:47,269 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,276 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,276 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-04 23:44:47,278 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed

2026-06-04 23:44:47,295 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed

2026-06-04 23:44:47,295 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok

2026-06-04 23:44:47,297 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,300 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,300 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok

2026-06-04 23:44:47,303 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,310 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,310 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok

2026-06-04 23:44:47,312 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,319 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,319 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok

2026-06-04 23:44:47,321 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:47,349 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:47,349 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/cp_consol_bam.ok

2026-06-04 23:44:47,352 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:48,699 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:48,699 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/index_consol_bam.ok

2026-06-04 23:44:48,701 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-04 23:45:21,147 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-04 23:45:21,147 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-04 23:45:21,149 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan

2026-06-04 23:45:21,786 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan

2026-06-04 23:45:21,786 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-04 23:45:21,788 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 

2026-06-04 23:45:21,912 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 

2026-06-04 23:45:21,912 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-04 23:45:21,914 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed

2026-06-04 23:45:21,963 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed

2026-06-04 23:45:21,963 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-04 23:45:21,965 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 

2026-06-04 23:45:22,006 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 

2026-06-04 23:45:22,006 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-04 23:45:22,008 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed

2026-06-04 23:45:22,030 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed

2026-06-04 23:45:22,030 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-04 23:45:22,032 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-04 23:45:22,085 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-04 23:45:22,085 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/add_splice_info.ok

2026-06-04 23:45:22,087 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-04 23:45:22,243 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.xUJ2ieXBIN/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-04 23:45:22,243 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/blast_filter.ok

2026-06-04 23:45:22,245 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir

2026-06-04 23:45:22,265 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir

2026-06-04 23:45:22,265 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/annot_filter.ok

2026-06-04 23:45:22,267 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-04 23:45:22,288 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-04 23:45:22,288 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/EM_adj_counts.ok

2026-06-04 23:45:22,290 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-04 23:50:52,893 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.51 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-04 23:50:52,893 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/add_FFPM.ok

2026-06-04 23:50:52,895 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/microH.dat

2026-06-04 23:50:53,099 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.xUJ2ieXBIN/fi_workdir/microH.dat

2026-06-04 23:50:53,099 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/microH.dat.ok

2026-06-04 23:50:53,101 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.xUJ2ieXBIN/fi_workdir/microH.dat /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-04 23:50:53,139 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.xUJ2ieXBIN/fi_workdir/microH.dat /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-04 23:50:53,139 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/append_microH_info.ok

2026-06-04 23:50:53,142 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv

2026-06-04 23:50:53,146 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv

2026-06-04 23:50:53,146 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/cp_final.ok

2026-06-04 23:50:53,149 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv

2026-06-04 23:50:53,164 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv

2026-06-04 23:50:53,164 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/final.abridged.ok

2026-06-04 23:50:53,166 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.xUJ2ieXBIN --json_outfile /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1

2026-06-04 23:50:53,187 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.xUJ2ieXBIN --json_outfile /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1

2026-06-04 23:50:53,187 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/create_fi_igvjs.ok

2026-06-04 23:50:53,189 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html

2026-06-04 23:50:53,934 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bGW-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html

2026-06-04 23:50:53,934 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/fusion_reports_html.ok

2026-06-04 23:50:53,936 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-04 23:50:53,967 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-04 23:50:53,967 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/fusion_annotator.ok

2026-06-04 23:50:53,969 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-04 23:50:54,129 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.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.xUJ2ieXBIN/ctat_genome_lib_build_dir > /tmp/nxf.xUJ2ieXBIN/659_bGW-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-04 23:50:54,129 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.xUJ2ieXBIN/chckpts_dir/fusion_coding_region_effect.ok