File Info

Filename
FusionInspector.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/aa054f7d1368c2f4dec6e24ab9cbba/FusionInspector.log
Size
43.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (659_d01-T1-TRNA-1_B23WHTKLT4_1)
Attempt

Content

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2026-06-08 09:36:48,529 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_d01-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 09:36:55,408 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_d01-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 09:36:55,408 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/fusion_contigs.ok

2026-06-08 09:36:55,409 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 09:36:55,412 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 09:36:55,412 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/cp_contigs_file_workdir

2026-06-08 09:36:55,413 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf

2026-06-08 09:36:55,416 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf

2026-06-08 09:36:55,416 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 09:36:55,418 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.GHpW07itJ7/cytoBand.txt

2026-06-08 09:36:55,443 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.GHpW07itJ7/cytoBand.txt

2026-06-08 09:36:55,443 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/cytoband.ok

2026-06-08 09:36:55,445 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed

2026-06-08 09:36:55,502 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed

2026-06-08 09:36:55,502 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 09:36:55,504 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 09:36:55,506 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 09:36:55,506 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok

2026-06-08 09:36:55,507 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 09:36:55,514 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed

2026-06-08 09:36:55,514 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok

2026-06-08 09:36:55,516 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz

2026-06-08 09:36:55,521 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz

2026-06-08 09:36:55,522 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok

2026-06-08 09:36:55,523 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 09:36:55,529 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa

2026-06-08 09:36:55,529 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/merged_contig_fai.ok

2026-06-08 09:36:55,530 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_d01-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.GHpW07itJ7/fi_workdir --reads "/tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"

2026-06-08 10:27:43,657 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 50.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_d01-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.GHpW07itJ7/fi_workdir --reads "/tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"

2026-06-08 10:27:43,657 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/run_STAR.ok

2026-06-08 10:27:43,660 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 10:27:45,990 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 10:27:45,990 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/mark_dup_reads.ok

2026-06-08 10:27:45,992 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 10:27:46,254 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 10:27:46,254 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 10:27:46,256 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 10:28:00,005 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 10:28:00,005 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 10:28:00,008 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 10:28:35,723 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 10:28:35,723 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 10:28:35,725 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary

2026-06-08 10:28:35,741 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary

2026-06-08 10:28:35,742 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 10:28:35,743 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 10:28:35,759 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 10:28:35,759 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 10:28:35,761 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 10:28:35,778 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 10:28:35,778 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 10:28:35,780 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 10:28:35,793 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 10:28:35,793 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 10:28:35,794 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"

2026-06-08 10:28:35,849 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"

2026-06-08 10:28:35,849 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 10:28:35,851 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam

2026-06-08 10:28:35,856 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam

2026-06-08 10:28:35,856 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 10:28:35,858 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed

2026-06-08 10:28:35,896 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed

2026-06-08 10:28:35,897 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok

2026-06-08 10:28:35,898 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,900 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,900 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok

2026-06-08 10:28:35,902 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,909 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,909 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok

2026-06-08 10:28:35,911 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 10:28:35,916 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 10:28:35,916 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok

2026-06-08 10:28:35,918 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 10:28:35,931 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 10:28:35,931 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/span_reads_acc.ok

2026-06-08 10:28:35,933 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 10:28:35,938 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 10:28:35,938 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 10:28:35,940 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : 

2026-06-08 10:28:35,955 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : 

2026-06-08 10:28:35,955 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_spanning_reads.ok

2026-06-08 10:28:35,956 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 10:28:35,961 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam

2026-06-08 10:28:35,961 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 10:28:35,962 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed

2026-06-08 10:28:35,977 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed

2026-06-08 10:28:35,977 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok

2026-06-08 10:28:35,978 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,980 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,980 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok

2026-06-08 10:28:35,981 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,986 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:28:35,986 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok

2026-06-08 10:28:35,988 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 10:28:35,992 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 10:28:35,993 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/659_d01-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok

2026-06-08 10:28:35,994 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 10:28:36,000 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 10:28:36,000 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/cp_consol_bam.ok

2026-06-08 10:28:36,002 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 10:28:36,261 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam

2026-06-08 10:28:36,262 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/index_consol_bam.ok

2026-06-08 10:28:36,263 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 10:28:43,110 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 10:28:43,110 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 10:28:43,112 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan

2026-06-08 10:28:43,238 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan

2026-06-08 10:28:43,238 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 10:28:43,240 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 

2026-06-08 10:28:43,279 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 

2026-06-08 10:28:43,279 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 10:28:43,280 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed

2026-06-08 10:28:43,309 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed

2026-06-08 10:28:43,309 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 10:28:43,311 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 

2026-06-08 10:28:43,334 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 

2026-06-08 10:28:43,334 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 10:28:43,336 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed

2026-06-08 10:28:43,357 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed

2026-06-08 10:28:43,357 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 10:28:43,359 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 10:28:43,384 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 10:28:43,384 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/add_splice_info.ok

2026-06-08 10:28:43,386 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 10:28:43,529 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.GHpW07itJ7/fi_workdir/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 10:28:43,530 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/blast_filter.ok

2026-06-08 10:28:43,531 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir

2026-06-08 10:28:43,548 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir

2026-06-08 10:28:43,548 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/annot_filter.ok

2026-06-08 10:28:43,550 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 10:28:43,565 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 10:28:43,565 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/EM_adj_counts.ok

2026-06-08 10:28:43,567 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 10:33:32,192 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 4.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 10:33:32,192 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/add_FFPM.ok

2026-06-08 10:33:32,194 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.GHpW07itJ7/fi_workdir/microH.dat

2026-06-08 10:33:32,247 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.GHpW07itJ7/fi_workdir/microH.dat

2026-06-08 10:33:32,247 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/microH.dat.ok

2026-06-08 10:33:32,249 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.GHpW07itJ7/fi_workdir/microH.dat /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 10:33:32,265 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.GHpW07itJ7/fi_workdir/microH.dat /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 10:33:32,265 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/append_microH_info.ok

2026-06-08 10:33:32,267 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv

2026-06-08 10:33:32,269 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv

2026-06-08 10:33:32,269 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/cp_final.ok

2026-06-08 10:33:32,270 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 10:33:32,283 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 10:33:32,283 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/final.abridged.ok

2026-06-08 10:33:32,285 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.GHpW07itJ7 --json_outfile /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_d01-T1-TRNA-1_B23WHTKLT4_1

2026-06-08 10:33:32,305 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.GHpW07itJ7 --json_outfile /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_d01-T1-TRNA-1_B23WHTKLT4_1

2026-06-08 10:33:32,305 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/create_fi_igvjs.ok

2026-06-08 10:33:32,307 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_d01-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html

2026-06-08 10:33:32,598 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_d01-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html

2026-06-08 10:33:32,598 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/fusion_reports_html.ok

2026-06-08 10:33:32,600 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 10:33:32,623 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 10:33:32,623 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/fusion_annotator.ok

2026-06-08 10:33:32,625 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 10:33:32,655 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.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.GHpW07itJ7/ctat_genome_lib_build_dir > /tmp/nxf.GHpW07itJ7/659_d01-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 10:33:32,656 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.GHpW07itJ7/chckpts_dir/fusion_coding_region_effect.ok