File Info

Filename
FusionInspector.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/d323520a02d12c33df121ef7c134a2/FusionInspector.log
Size
44.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt

Content

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2026-06-08 11:40:43,741 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 

2026-06-08 11:40:51,204 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 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 

2026-06-08 11:40:51,204 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/fusion_contigs.ok

2026-06-08 11:40:51,206 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa

2026-06-08 11:40:51,209 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa

2026-06-08 11:40:51,209 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/cp_contigs_file_workdir

2026-06-08 11:40:51,210 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf

2026-06-08 11:40:51,213 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf

2026-06-08 11:40:51,214 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 11:40:51,215 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.NoKAY250U1/cytoBand.txt

2026-06-08 11:40:51,279 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.NoKAY250U1/cytoBand.txt

2026-06-08 11:40:51,279 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/cytoband.ok

2026-06-08 11:40:51,281 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed

2026-06-08 11:40:51,434 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed

2026-06-08 11:40:51,434 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 11:40:51,436 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed

2026-06-08 11:40:51,438 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed

2026-06-08 11:40:51,438 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok

2026-06-08 11:40:51,440 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed

2026-06-08 11:40:51,448 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed

2026-06-08 11:40:51,448 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok

2026-06-08 11:40:51,450 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz

2026-06-08 11:40:51,456 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz

2026-06-08 11:40:51,456 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok

2026-06-08 11:40:51,458 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa

2026-06-08 11:40:51,465 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa

2026-06-08 11:40:51,466 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/merged_contig_fai.ok

2026-06-08 11:40:51,467 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.NoKAY250U1/fi_workdir --reads "/tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"

2026-06-08 12:39:12,143 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 58.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.NoKAY250U1/fi_workdir --reads "/tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"

2026-06-08 12:39:12,143 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/run_STAR.ok

2026-06-08 12:39:12,145 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 12:39:30,237 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 12:39:30,237 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/mark_dup_reads.ok

2026-06-08 12:39:30,239 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam

2026-06-08 12:39:32,473 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam

2026-06-08 12:39:32,473 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 12:39:32,475 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 12:41:31,749 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 1.99 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 12:41:31,749 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 12:41:31,751 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 12:47:15,104 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.72 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 12:47:15,104 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 12:47:15,107 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary

2026-06-08 12:47:15,299 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary

2026-06-08 12:47:15,299 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 12:47:15,301 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj

2026-06-08 12:47:15,342 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj

2026-06-08 12:47:15,343 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 12:47:15,344 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 12:47:15,371 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 12:47:15,371 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 12:47:15,373 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 12:47:15,393 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 12:47:15,393 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 12:47:15,395 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"

2026-06-08 12:47:15,474 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"

2026-06-08 12:47:15,474 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 12:47:15,476 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam

2026-06-08 12:47:15,485 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam

2026-06-08 12:47:15,485 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 12:47:15,486 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed

2026-06-08 12:47:15,599 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed

2026-06-08 12:47:15,599 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok

2026-06-08 12:47:15,601 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,604 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,605 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok

2026-06-08 12:47:15,606 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,618 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,618 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok

2026-06-08 12:47:15,620 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 12:47:15,626 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 12:47:15,626 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok

2026-06-08 12:47:15,628 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 12:47:15,648 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 12:47:15,648 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/span_reads_acc.ok

2026-06-08 12:47:15,650 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam

2026-06-08 12:47:15,655 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam

2026-06-08 12:47:15,655 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 12:47:15,657 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : 

2026-06-08 12:47:15,694 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : 

2026-06-08 12:47:15,694 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_spanning_reads.ok

2026-06-08 12:47:15,695 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam

2026-06-08 12:47:15,700 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam

2026-06-08 12:47:15,700 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 12:47:15,701 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed

2026-06-08 12:47:15,716 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed

2026-06-08 12:47:15,717 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok

2026-06-08 12:47:15,718 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,720 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,720 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok

2026-06-08 12:47:15,722 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,727 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 12:47:15,727 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok

2026-06-08 12:47:15,728 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 12:47:15,734 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 12:47:15,734 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok

2026-06-08 12:47:15,735 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam

2026-06-08 12:47:15,770 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam

2026-06-08 12:47:15,770 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/cp_consol_bam.ok

2026-06-08 12:47:15,771 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam

2026-06-08 12:47:18,001 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam

2026-06-08 12:47:18,001 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/index_consol_bam.ok

2026-06-08 12:47:18,003 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 

2026-06-08 12:48:14,219 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.94 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 

2026-06-08 12:48:14,219 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 12:48:14,221 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan

2026-06-08 12:48:15,291 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan

2026-06-08 12:48:15,291 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 12:48:15,293 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 

2026-06-08 12:48:15,394 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 

2026-06-08 12:48:15,394 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 12:48:15,395 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed

2026-06-08 12:48:15,447 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed

2026-06-08 12:48:15,447 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 12:48:15,449 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 

2026-06-08 12:48:15,485 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 

2026-06-08 12:48:15,485 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 12:48:15,487 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed

2026-06-08 12:48:15,508 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed

2026-06-08 12:48:15,508 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 12:48:15,510 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 12:48:15,564 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 12:48:15,564 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/add_splice_info.ok

2026-06-08 12:48:15,566 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 12:48:15,716 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.NoKAY250U1/fi_workdir/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 12:48:15,716 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/blast_filter.ok

2026-06-08 12:48:15,718 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir

2026-06-08 12:48:15,739 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir

2026-06-08 12:48:15,739 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/annot_filter.ok

2026-06-08 12:48:15,740 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 12:48:15,763 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 12:48:15,763 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/EM_adj_counts.ok

2026-06-08 12:48:15,765 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 12:53:50,694 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.58 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 12:53:50,695 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/add_FFPM.ok

2026-06-08 12:53:50,697 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf  > /tmp/nxf.NoKAY250U1/fi_workdir/microH.dat

2026-06-08 12:53:50,890 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.gtf  > /tmp/nxf.NoKAY250U1/fi_workdir/microH.dat

2026-06-08 12:53:50,890 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/microH.dat.ok

2026-06-08 12:53:50,892 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.NoKAY250U1/fi_workdir/microH.dat /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 12:53:50,934 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.NoKAY250U1/fi_workdir/microH.dat /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 12:53:50,934 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/append_microH_info.ok

2026-06-08 12:53:50,935 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv

2026-06-08 12:53:50,938 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv

2026-06-08 12:53:50,938 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/cp_final.ok

2026-06-08 12:53:50,940 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv

2026-06-08 12:53:50,954 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv

2026-06-08 12:53:50,954 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/final.abridged.ok

2026-06-08 12:53:50,956 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.NoKAY250U1 --json_outfile /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2

2026-06-08 12:53:50,976 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.NoKAY250U1 --json_outfile /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2

2026-06-08 12:53:50,977 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/create_fi_igvjs.ok

2026-06-08 12:53:50,978 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html

2026-06-08 12:53:51,734 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html

2026-06-08 12:53:51,734 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/fusion_reports_html.ok

2026-06-08 12:53:51,736 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 12:53:51,766 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 12:53:51,767 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/fusion_annotator.ok

2026-06-08 12:53:51,768 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 12:53:51,842 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.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.NoKAY250U1/ctat_genome_lib_build_dir > /tmp/nxf.NoKAY250U1/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 12:53:51,842 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.NoKAY250U1/chckpts_dir/fusion_coding_region_effect.ok