FusionInspector.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (GM24385_0001_RNA_0001_23H5VFLT4_s24)

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/ed96f47b21142c700e79fd65d25490/FusionInspector.log
Size: 44.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (GM24385_0001_RNA_0001_23H5VFLT4_s24)
Attempt
Content

2026-06-08 08:56:09,105 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions GM24385_0001_RNA_0001_23H5VFLT4_s24.fusionreport.tsv --gtf /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24 --shrink_introns --max_intron_length 1000 

2026-06-08 08:56:15,841 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 GM24385_0001_RNA_0001_23H5VFLT4_s24.fusionreport.tsv --gtf /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24 --shrink_introns --max_intron_length 1000 

2026-06-08 08:56:15,842 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/fusion_contigs.ok

2026-06-08 08:56:15,844 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa

2026-06-08 08:56:15,846 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa

2026-06-08 08:56:15,846 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/cp_contigs_file_workdir

2026-06-08 08:56:15,848 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf

2026-06-08 08:56:15,850 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf

2026-06-08 08:56:15,850 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 08:56:15,852 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf > /tmp/nxf.law0MS1VGz/cytoBand.txt

2026-06-08 08:56:15,867 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf > /tmp/nxf.law0MS1VGz/cytoBand.txt

2026-06-08 08:56:15,867 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/cytoband.ok

2026-06-08 08:56:15,869 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed

2026-06-08 08:56:15,911 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed

2026-06-08 08:56:15,911 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 08:56:15,913 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.sorted.bed

2026-06-08 08:56:15,915 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.sorted.bed

2026-06-08 08:56:15,915 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.bedsort.ok

2026-06-08 08:56:15,917 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.sorted.bed

2026-06-08 08:56:15,923 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.sorted.bed

2026-06-08 08:56:15,923 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.bgzip.ok

2026-06-08 08:56:15,925 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.sorted.bed.gz

2026-06-08 08:56:15,931 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.sorted.bed.gz

2026-06-08 08:56:15,931 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.bed.tabix.ok

2026-06-08 08:56:15,933 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa

2026-06-08 08:56:15,937 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa

2026-06-08 08:56:15,938 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/merged_contig_fai.ok

2026-06-08 08:56:15,939 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa --max_mate_dist 100000 -G /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf --CPU 8 --out_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24.star --out_dir /tmp/nxf.law0MS1VGz/fi_workdir --reads "/tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24_1.fastp.fastq.gz /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24_2.fastp.fastq.gz"

2026-06-08 09:41:23,522 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 45.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa --max_mate_dist 100000 -G /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf --CPU 8 --out_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24.star --out_dir /tmp/nxf.law0MS1VGz/fi_workdir --reads "/tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24_1.fastp.fastq.gz /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24_2.fastp.fastq.gz"

2026-06-08 09:41:23,522 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/run_STAR.ok

2026-06-08 09:41:23,524 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.sortedByCoord.out.bam   -o /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 09:41:24,172 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.sortedByCoord.out.bam   -o /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 09:41:24,173 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/mark_dup_reads.ok

2026-06-08 09:41:24,174 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam

2026-06-08 09:41:24,250 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam

2026-06-08 09:41:24,251 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 09:41:24,252 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 09:41:27,549 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 09:41:27,549 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 09:41:27,552 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 09:41:36,971 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 09:41:36,971 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 09:41:36,973 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary

2026-06-08 09:41:36,988 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary

2026-06-08 09:41:36,988 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 09:41:36,989 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj

2026-06-08 09:41:37,003 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj

2026-06-08 09:41:37,003 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 09:41:37,005 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 09:41:37,022 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 09:41:37,023 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 09:41:37,024 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 09:41:37,036 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 09:41:37,036 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 09:41:37,038 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa -  | samtools sort -@ 8 - -o /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam"

2026-06-08 09:41:37,076 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa -  | samtools sort -@ 8 - -o /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam"

2026-06-08 09:41:37,076 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 09:41:37,078 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam

2026-06-08 09:41:37,083 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam

2026-06-08 09:41:37,083 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 09:41:37,084 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed

2026-06-08 09:41:37,104 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed

2026-06-08 09:41:37,104 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bam_to_bed.ok

2026-06-08 09:41:37,106 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,107 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,108 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bedsort.ok

2026-06-08 09:41:37,109 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,115 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,115 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bgzip.ok

2026-06-08 09:41:37,116 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 09:41:37,122 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 09:41:37,122 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.junction_reads.bam.tabix.ok

2026-06-08 09:41:37,124 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 09:41:37,136 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 09:41:37,136 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/span_reads_acc.ok

2026-06-08 09:41:37,138 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam

2026-06-08 09:41:37,143 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam

2026-06-08 09:41:37,143 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 09:41:37,145 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa -  | samtools sort -@ 8 - -o /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam || : 

2026-06-08 09:41:37,181 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa -  | samtools sort -@ 8 - -o /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam || : 

2026-06-08 09:41:37,181 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_spanning_reads.ok

2026-06-08 09:41:37,183 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam

2026-06-08 09:41:37,187 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam

2026-06-08 09:41:37,188 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 09:41:37,189 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed

2026-06-08 09:41:37,204 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed

2026-06-08 09:41:37,204 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bam_to_bed.ok

2026-06-08 09:41:37,206 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,207 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,207 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bedsort.ok

2026-06-08 09:41:37,209 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,213 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed.sorted.bed

2026-06-08 09:41:37,214 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bgzip.ok

2026-06-08 09:41:37,215 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 09:41:37,220 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 09:41:37,220 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s24.spanning_reads.bam.tabix.ok

2026-06-08 09:41:37,222 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam

2026-06-08 09:41:37,225 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.star.cSorted.dupsMarked.bam /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam

2026-06-08 09:41:37,225 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/cp_consol_bam.ok

2026-06-08 09:41:37,226 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam

2026-06-08 09:41:37,301 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam

2026-06-08 09:41:37,301 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/index_consol_bam.ok

2026-06-08 09:41:37,303 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam --max_insert_size 10000000 

2026-06-08 09:41:39,019 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam --max_insert_size 10000000 

2026-06-08 09:41:39,019 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 09:41:39,021 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam.frag_coords > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.FusionJuncSpan

2026-06-08 09:41:39,064 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.consolidated.bam.frag_coords > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.FusionJuncSpan

2026-06-08 09:41:39,064 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 09:41:39,066 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.Pfam.gff3 

2026-06-08 09:41:39,094 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.Pfam.gff3 

2026-06-08 09:41:39,095 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 09:41:39,096 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.Pfam.gff3 > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.Pfam.bed

2026-06-08 09:41:39,119 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.Pfam.gff3 > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.Pfam.bed

2026-06-08 09:41:39,119 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 09:41:39,121 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.seqsimilar.gff3 

2026-06-08 09:41:39,143 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.seqsimilar.gff3 

2026-06-08 09:41:39,143 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 09:41:39,145 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.seqsimilar.gff3 > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.seqsimilar.bed

2026-06-08 09:41:39,165 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.seqsimilar.gff3 > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.igv.seqsimilar.bed

2026-06-08 09:41:39,165 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 09:41:39,167 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 09:41:39,182 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa > /tmp/nxf.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 09:41:39,182 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/add_splice_info.ok

2026-06-08 09:41:39,184 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 09:41:39,327 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.law0MS1VGz/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 09:41:39,327 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/blast_filter.ok

2026-06-08 09:41:39,328 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir

2026-06-08 09:41:39,346 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir

2026-06-08 09:41:39,346 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/annot_filter.ok

2026-06-08 09:41:39,348 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 09:41:39,362 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 09:41:39,362 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/EM_adj_counts.ok

2026-06-08 09:41:39,364 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24_1.fastp.fastq.gz /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 09:46:02,885 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 4.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24_1.fastp.fastq.gz /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 09:46:02,885 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/add_FFPM.ok

2026-06-08 09:46:02,887 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa --gtf /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf  > /tmp/nxf.law0MS1VGz/fi_workdir/microH.dat

2026-06-08 09:46:02,912 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fa --gtf /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.gtf  > /tmp/nxf.law0MS1VGz/fi_workdir/microH.dat

2026-06-08 09:46:02,913 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/microH.dat.ok

2026-06-08 09:46:02,914 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.law0MS1VGz/fi_workdir/microH.dat /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 09:46:02,930 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.law0MS1VGz/fi_workdir/microH.dat /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 09:46:02,931 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/append_microH_info.ok

2026-06-08 09:46:02,933 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.tsv

2026-06-08 09:46:02,935 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.tsv

2026-06-08 09:46:02,935 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/cp_final.ok

2026-06-08 09:46:02,936 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv

2026-06-08 09:46:02,949 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv

2026-06-08 09:46:02,949 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/final.abridged.ok

2026-06-08 09:46:02,951 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.law0MS1VGz --json_outfile /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_inspector_web.json --file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24

2026-06-08 09:46:02,971 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.law0MS1VGz --json_outfile /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_inspector_web.json --file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24

2026-06-08 09:46:02,971 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/create_fi_igvjs.ok

2026-06-08 09:46:02,973 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_inspector_web.json --input_file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24 --html_output /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_inspector_web.html

2026-06-08 09:46:03,100 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_inspector_web.json --input_file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s24 --html_output /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.fusion_inspector_web.html

2026-06-08 09:46:03,100 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/fusion_reports_html.ok

2026-06-08 09:46:03,102 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 09:46:03,123 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 09:46:03,123 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/fusion_annotator.ok

2026-06-08 09:46:03,126 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 09:46:03,153 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.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.law0MS1VGz/ctat_genome_lib_build_dir > /tmp/nxf.law0MS1VGz/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 09:46:03,153 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.law0MS1VGz/chckpts_dir/fusion_coding_region_effect.ok