File Info

Filename
FusionInspector.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/3f2999a8544b0778e9aec04bd11dc4/FusionInspector.log
Size
43.8 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (tih_rna_sample_00116_B23WHTKLT4_2)
Attempt

Content

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2026-06-08 09:52:48,362 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00116_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 

2026-06-08 09:52:55,327 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 tih_rna_sample_00116_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 

2026-06-08 09:52:55,327 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/fusion_contigs.ok

2026-06-08 09:52:55,329 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fa

2026-06-08 09:52:55,332 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fa

2026-06-08 09:52:55,332 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/cp_contigs_file_workdir

2026-06-08 09:52:55,334 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf

2026-06-08 09:52:55,336 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf

2026-06-08 09:52:55,336 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 09:52:55,338 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf > /tmp/nxf.zYE8v3APVY/cytoBand.txt

2026-06-08 09:52:55,403 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf > /tmp/nxf.zYE8v3APVY/cytoBand.txt

2026-06-08 09:52:55,403 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/cytoband.ok

2026-06-08 09:52:55,405 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed

2026-06-08 09:52:55,473 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed

2026-06-08 09:52:55,473 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 09:52:55,475 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed.sorted.bed

2026-06-08 09:52:55,477 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed.sorted.bed

2026-06-08 09:52:55,477 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.bed.bedsort.ok

2026-06-08 09:52:55,479 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed.sorted.bed

2026-06-08 09:52:55,486 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed.sorted.bed

2026-06-08 09:52:55,486 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.bed.bgzip.ok

2026-06-08 09:52:55,488 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed.sorted.bed.gz

2026-06-08 09:52:55,494 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.bed.sorted.bed.gz

2026-06-08 09:52:55,494 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.bed.tabix.ok

2026-06-08 09:52:55,496 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa

2026-06-08 09:52:55,505 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa

2026-06-08 09:52:55,505 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/merged_contig_fai.ok

2026-06-08 09:52:55,507 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00116_B23WHTKLT4_2.star --out_dir /tmp/nxf.zYE8v3APVY/fi_workdir --reads "/tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2_2.fastp.fastq.gz"

2026-06-08 10:59:44,314 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 66.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00116_B23WHTKLT4_2.star --out_dir /tmp/nxf.zYE8v3APVY/fi_workdir --reads "/tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2_2.fastp.fastq.gz"

2026-06-08 10:59:44,314 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/run_STAR.ok

2026-06-08 10:59:44,316 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:00:28,754 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:00:28,754 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/mark_dup_reads.ok

2026-06-08 11:00:28,756 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

2026-06-08 11:00:33,956 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

2026-06-08 11:00:33,956 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 11:00:33,958 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:05:47,116 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:05:47,116 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 11:05:47,119 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:15:58,654 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 10.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:15:58,655 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 11:15:58,657 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary

2026-06-08 11:15:58,675 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary

2026-06-08 11:15:58,675 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 11:15:58,676 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:15:58,720 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:15:58,720 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 11:15:58,722 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:15:58,740 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:15:58,740 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 11:15:58,741 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:15:58,755 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:15:58,755 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 11:15:58,756 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam"

2026-06-08 11:15:58,819 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam"

2026-06-08 11:15:58,819 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 11:15:58,821 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam

2026-06-08 11:15:58,827 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam

2026-06-08 11:15:58,828 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 11:15:58,830 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed

2026-06-08 11:15:58,892 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed

2026-06-08 11:15:58,893 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok

2026-06-08 11:15:58,894 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 11:15:58,897 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 11:15:58,897 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bedsort.ok

2026-06-08 11:15:58,899 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 11:15:58,906 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed

2026-06-08 11:15:58,906 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bgzip.ok

2026-06-08 11:15:58,908 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:15:58,913 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:15:58,914 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.junction_reads.bam.tabix.ok

2026-06-08 11:15:58,915 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:15:58,928 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:15:58,928 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/span_reads_acc.ok

2026-06-08 11:15:58,930 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam

2026-06-08 11:15:58,935 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam

2026-06-08 11:15:58,935 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 11:15:58,937 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam || : 

2026-06-08 11:15:58,973 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam || : 

2026-06-08 11:15:58,973 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_spanning_reads.ok

2026-06-08 11:15:58,975 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam

2026-06-08 11:15:58,980 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam

2026-06-08 11:15:58,980 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 11:15:58,982 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed

2026-06-08 11:15:58,996 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed

2026-06-08 11:15:58,996 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok

2026-06-08 11:15:58,998 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:15:58,999 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:15:58,999 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok

2026-06-08 11:15:59,001 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:15:59,005 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:15:59,005 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok

2026-06-08 11:15:59,007 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:15:59,012 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:15:59,012 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/tih_rna_sample_00116_B23WHTKLT4_2.spanning_reads.bam.tabix.ok

2026-06-08 11:15:59,014 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam

2026-06-08 11:15:59,091 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam

2026-06-08 11:15:59,091 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/cp_consol_bam.ok

2026-06-08 11:15:59,092 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam

2026-06-08 11:16:04,261 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam

2026-06-08 11:16:04,262 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/index_consol_bam.ok

2026-06-08 11:16:04,264 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:18:29,752 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 2.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:18:29,752 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 11:18:29,754 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.FusionJuncSpan

2026-06-08 11:18:32,297 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.FusionJuncSpan

2026-06-08 11:18:32,298 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 11:18:32,300 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.Pfam.gff3 

2026-06-08 11:18:32,340 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.Pfam.gff3 

2026-06-08 11:18:32,340 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 11:18:32,342 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.Pfam.bed

2026-06-08 11:18:32,371 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.Pfam.bed

2026-06-08 11:18:32,371 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 11:18:32,373 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.seqsimilar.gff3 

2026-06-08 11:18:32,398 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.seqsimilar.gff3 

2026-06-08 11:18:32,398 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 11:18:32,400 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.seqsimilar.bed

2026-06-08 11:18:32,421 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.igv.seqsimilar.bed

2026-06-08 11:18:32,421 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 11:18:32,423 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:18:32,484 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa > /tmp/nxf.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:18:32,484 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/add_splice_info.ok

2026-06-08 11:18:32,486 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:18:32,629 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.zYE8v3APVY/fi_workdir/tih_rna_sample_00116_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:18:32,629 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/blast_filter.ok

2026-06-08 11:18:32,631 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir

2026-06-08 11:18:32,649 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir

2026-06-08 11:18:32,649 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/annot_filter.ok

2026-06-08 11:18:32,650 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:18:32,666 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:18:32,666 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/EM_adj_counts.ok

2026-06-08 11:18:32,668 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:23:49,274 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:23:49,274 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/add_FFPM.ok

2026-06-08 11:23:49,276 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa --gtf /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf  > /tmp/nxf.zYE8v3APVY/fi_workdir/microH.dat

2026-06-08 11:23:49,509 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fa --gtf /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.gtf  > /tmp/nxf.zYE8v3APVY/fi_workdir/microH.dat

2026-06-08 11:23:49,509 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/microH.dat.ok

2026-06-08 11:23:49,511 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.zYE8v3APVY/fi_workdir/microH.dat /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:23:49,536 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.zYE8v3APVY/fi_workdir/microH.dat /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:23:49,536 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/append_microH_info.ok

2026-06-08 11:23:49,538 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.tsv

2026-06-08 11:23:49,540 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.tsv

2026-06-08 11:23:49,540 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/cp_final.ok

2026-06-08 11:23:49,542 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv

2026-06-08 11:23:49,555 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv

2026-06-08 11:23:49,555 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/final.abridged.ok

2026-06-08 11:23:49,557 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.zYE8v3APVY --json_outfile /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00116_B23WHTKLT4_2

2026-06-08 11:23:49,577 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.zYE8v3APVY --json_outfile /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00116_B23WHTKLT4_2

2026-06-08 11:23:49,577 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/create_fi_igvjs.ok

2026-06-08 11:23:49,579 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00116_B23WHTKLT4_2 --html_output /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fusion_inspector_web.html

2026-06-08 11:23:50,507 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00116_B23WHTKLT4_2 --html_output /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.fusion_inspector_web.html

2026-06-08 11:23:50,507 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/fusion_reports_html.ok

2026-06-08 11:23:50,508 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:23:50,530 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:23:50,531 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/fusion_annotator.ok

2026-06-08 11:23:50,532 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:23:50,561 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.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.zYE8v3APVY/ctat_genome_lib_build_dir > /tmp/nxf.zYE8v3APVY/tih_rna_sample_00116_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:23:50,561 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.zYE8v3APVY/chckpts_dir/fusion_coding_region_effect.ok