2026-06-04 22:09:06,395 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 

2026-06-04 22:09:20,020 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 

2026-06-04 22:09:20,021 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/fusion_contigs.ok

2026-06-04 22:09:20,025 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:09:20,030 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:09:20,031 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/cp_contigs_file_workdir

2026-06-04 22:09:20,035 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf

2026-06-04 22:09:20,043 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf

2026-06-04 22:09:20,043 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-04 22:09:20,046 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.m2yAExSUue/cytoBand.txt

2026-06-04 22:09:20,204 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.m2yAExSUue/cytoBand.txt

2026-06-04 22:09:20,204 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/cytoband.ok

2026-06-04 22:09:20,215 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed

2026-06-04 22:09:20,548 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed

2026-06-04 22:09:20,549 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-04 22:09:20,553 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:09:20,560 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:09:20,560 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok

2026-06-04 22:09:20,564 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:09:20,596 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-04 22:09:20,597 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok

2026-06-04 22:09:20,615 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz

2026-06-04 22:09:20,637 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz

2026-06-04 22:09:20,637 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok

2026-06-04 22:09:20,641 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:09:20,680 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-04 22:09:20,681 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/merged_contig_fai.ok

2026-06-04 22:09:20,684 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.m2yAExSUue/fi_workdir --reads "/tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"

2026-06-04 23:39:47,192 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 90.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.m2yAExSUue/fi_workdir --reads "/tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"

2026-06-04 23:39:47,193 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/run_STAR.ok

2026-06-04 23:39:47,196 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-04 23:39:59,509 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-04 23:39:59,509 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/mark_dup_reads.ok

2026-06-04 23:39:59,513 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

2026-06-04 23:40:01,049 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

2026-06-04 23:40:01,049 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/mark_dups_reads.index.ok

2026-06-04 23:40:01,053 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-04 23:41:15,820 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 1.25 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-04 23:41:15,820 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-04 23:41:15,824 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-04 23:44:46,965 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 3.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-04 23:44:46,965 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-04 23:44:46,968 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary

2026-06-04 23:44:47,038 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary

2026-06-04 23:44:47,038 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/coalesce_junc_n_span.ok

2026-06-04 23:44:47,041 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-04 23:44:47,070 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-04 23:44:47,070 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/init_EM_adj_counts.ok

2026-06-04 23:44:47,072 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-04 23:44:47,096 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-04 23:44:47,096 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/filter_by_frag_threshs.ok

2026-06-04 23:44:47,098 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-04 23:44:47,114 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-04 23:44:47,114 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-04 23:44:47,117 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"

2026-06-04 23:44:47,191 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"

2026-06-04 23:44:47,191 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-04 23:44:47,193 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam

2026-06-04 23:44:47,203 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam

2026-06-04 23:44:47,203 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-04 23:44:47,205 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed

2026-06-04 23:44:47,288 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed

2026-06-04 23:44:47,288 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok

2026-06-04 23:44:47,290 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,294 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,294 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok

2026-06-04 23:44:47,296 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,308 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,308 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok

2026-06-04 23:44:47,310 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,317 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,317 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok

2026-06-04 23:44:47,320 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-04 23:44:47,336 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-04 23:44:47,336 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/span_reads_acc.ok

2026-06-04 23:44:47,338 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,345 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,345 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/init_spanning_reads_bam.ok

2026-06-04 23:44:47,347 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 

2026-06-04 23:44:47,387 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 

2026-06-04 23:44:47,387 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_spanning_reads.ok

2026-06-04 23:44:47,389 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,395 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-04 23:44:47,396 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-04 23:44:47,398 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed

2026-06-04 23:44:47,415 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed

2026-06-04 23:44:47,415 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok

2026-06-04 23:44:47,417 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,420 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,420 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok

2026-06-04 23:44:47,422 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,428 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-04 23:44:47,428 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok

2026-06-04 23:44:47,430 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,437 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-04 23:44:47,437 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok

2026-06-04 23:44:47,439 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:47,480 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:47,480 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/cp_consol_bam.ok

2026-06-04 23:44:47,483 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:49,004 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-04 23:44:49,004 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/index_consol_bam.ok

2026-06-04 23:44:49,007 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-04 23:45:23,104 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.57 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-04 23:45:23,105 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-04 23:45:23,108 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan

2026-06-04 23:45:23,686 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan

2026-06-04 23:45:23,686 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-04 23:45:23,689 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 

2026-06-04 23:45:23,795 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 

2026-06-04 23:45:23,796 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-04 23:45:23,798 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed

2026-06-04 23:45:23,849 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed

2026-06-04 23:45:23,849 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-04 23:45:23,852 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 

2026-06-04 23:45:23,893 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 

2026-06-04 23:45:23,893 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-04 23:45:23,896 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed

2026-06-04 23:45:23,918 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed

2026-06-04 23:45:23,918 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-04 23:45:23,921 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-04 23:45:23,988 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-04 23:45:23,988 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/add_splice_info.ok

2026-06-04 23:45:23,991 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-04 23:45:24,159 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.m2yAExSUue/fi_workdir/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-04 23:45:24,159 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/blast_filter.ok

2026-06-04 23:45:24,161 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir

2026-06-04 23:45:24,185 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir

2026-06-04 23:45:24,185 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/annot_filter.ok

2026-06-04 23:45:24,188 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-04 23:45:24,216 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-04 23:45:24,217 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/EM_adj_counts.ok

2026-06-04 23:45:24,219 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-04 23:51:26,730 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 6.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-04 23:51:26,730 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/add_FFPM.ok

2026-06-04 23:51:26,733 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.m2yAExSUue/fi_workdir/microH.dat

2026-06-04 23:51:26,957 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.m2yAExSUue/fi_workdir/microH.dat

2026-06-04 23:51:26,958 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/microH.dat.ok

2026-06-04 23:51:26,960 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.m2yAExSUue/fi_workdir/microH.dat /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-04 23:51:27,029 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.m2yAExSUue/fi_workdir/microH.dat /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-04 23:51:27,030 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/append_microH_info.ok

2026-06-04 23:51:27,032 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv

2026-06-04 23:51:27,036 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv

2026-06-04 23:51:27,036 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/cp_final.ok

2026-06-04 23:51:27,038 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv

2026-06-04 23:51:27,055 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv

2026-06-04 23:51:27,055 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/final.abridged.ok

2026-06-04 23:51:27,057 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.m2yAExSUue --json_outfile /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1

2026-06-04 23:51:27,080 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.m2yAExSUue --json_outfile /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1

2026-06-04 23:51:27,080 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/create_fi_igvjs.ok

2026-06-04 23:51:27,082 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html

2026-06-04 23:51:28,122 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html

2026-06-04 23:51:28,122 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/fusion_reports_html.ok

2026-06-04 23:51:28,124 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-04 23:51:28,156 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-04 23:51:28,156 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/fusion_annotator.ok

2026-06-04 23:51:28,158 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-04 23:51:28,286 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.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.m2yAExSUue/ctat_genome_lib_build_dir > /tmp/nxf.m2yAExSUue/659_bIB-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-04 23:51:28,286 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.m2yAExSUue/chckpts_dir/fusion_coding_region_effect.ok