File Info

Filename
FusionInspector.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/93202e58d5142714636fd130154445/FusionInspector.log
Size
44.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt

Content

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2026-06-08 13:58:48,554 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 13:58:55,829 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 13:58:55,829 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_contigs.ok

2026-06-08 13:58:55,832 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa

2026-06-08 13:58:55,834 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa

2026-06-08 13:58:55,834 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_contigs_file_workdir

2026-06-08 13:58:55,836 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf

2026-06-08 13:58:55,839 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf

2026-06-08 13:58:55,839 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 13:58:55,841 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/cytoBand.txt

2026-06-08 13:58:55,893 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/cytoBand.txt

2026-06-08 13:58:55,893 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cytoband.ok

2026-06-08 13:58:55,895 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed

2026-06-08 13:58:56,020 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed

2026-06-08 13:58:56,020 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 13:58:56,022 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed

2026-06-08 13:58:56,025 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed

2026-06-08 13:58:56,025 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok

2026-06-08 13:58:56,027 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed

2026-06-08 13:58:56,035 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed

2026-06-08 13:58:56,035 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok

2026-06-08 13:58:56,037 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz

2026-06-08 13:58:56,043 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz

2026-06-08 13:58:56,043 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok

2026-06-08 13:58:56,045 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa

2026-06-08 13:58:56,053 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa

2026-06-08 13:58:56,053 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/merged_contig_fai.ok

2026-06-08 13:58:56,055 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.atNtBlHYmi/fi_workdir --reads "/tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"

2026-06-08 14:46:16,294 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 47.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.atNtBlHYmi/fi_workdir --reads "/tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"

2026-06-08 14:46:16,294 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/run_STAR.ok

2026-06-08 14:46:16,296 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 14:46:38,719 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 14:46:38,719 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/mark_dup_reads.ok

2026-06-08 14:46:38,722 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 14:46:41,540 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

2026-06-08 14:46:41,540 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 14:46:41,542 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 14:49:22,354 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 2.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 14:49:22,355 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 14:49:22,357 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 14:56:11,813 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 6.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 14:56:11,814 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 14:56:11,816 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary

2026-06-08 14:56:11,966 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary

2026-06-08 14:56:11,966 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 14:56:11,968 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 14:56:12,190 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 14:56:12,190 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 14:56:12,192 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 14:56:12,219 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 14:56:12,219 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 14:56:12,221 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 14:56:12,241 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 14:56:12,242 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 14:56:12,243 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"

2026-06-08 14:56:12,348 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"

2026-06-08 14:56:12,348 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 14:56:12,350 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam

2026-06-08 14:56:12,362 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam

2026-06-08 14:56:12,363 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 14:56:12,364 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed

2026-06-08 14:56:12,554 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed

2026-06-08 14:56:12,554 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok

2026-06-08 14:56:12,556 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,561 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,561 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok

2026-06-08 14:56:12,563 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,580 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,580 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok

2026-06-08 14:56:12,582 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 14:56:12,590 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 14:56:12,590 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok

2026-06-08 14:56:12,592 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 14:56:12,612 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 14:56:12,612 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/span_reads_acc.ok

2026-06-08 14:56:12,614 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam

2026-06-08 14:56:12,619 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam

2026-06-08 14:56:12,619 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 14:56:12,621 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 

2026-06-08 14:56:12,659 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 

2026-06-08 14:56:12,659 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_spanning_reads.ok

2026-06-08 14:56:12,661 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam

2026-06-08 14:56:12,666 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam

2026-06-08 14:56:12,666 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 14:56:12,668 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed

2026-06-08 14:56:12,684 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed

2026-06-08 14:56:12,684 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok

2026-06-08 14:56:12,686 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,688 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,688 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok

2026-06-08 14:56:12,690 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,695 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 14:56:12,695 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok

2026-06-08 14:56:12,697 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 14:56:12,702 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 14:56:12,702 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok

2026-06-08 14:56:12,704 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam

2026-06-08 14:56:12,749 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam

2026-06-08 14:56:12,749 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_consol_bam.ok

2026-06-08 14:56:12,751 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam

2026-06-08 14:56:15,558 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam

2026-06-08 14:56:15,558 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/index_consol_bam.ok

2026-06-08 14:56:15,561 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 14:57:31,120 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 1.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 14:57:31,120 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 14:57:31,122 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan

2026-06-08 14:57:32,606 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan

2026-06-08 14:57:32,606 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 14:57:32,608 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 

2026-06-08 14:57:32,699 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 

2026-06-08 14:57:32,699 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 14:57:32,701 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed

2026-06-08 14:57:32,752 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed

2026-06-08 14:57:32,752 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 14:57:32,754 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 

2026-06-08 14:57:32,786 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 

2026-06-08 14:57:32,786 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 14:57:32,788 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed

2026-06-08 14:57:32,810 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed

2026-06-08 14:57:32,810 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 14:57:32,812 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 14:57:32,859 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 14:57:32,859 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/add_splice_info.ok

2026-06-08 14:57:32,861 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 14:57:33,017 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 14:57:33,017 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/blast_filter.ok

2026-06-08 14:57:33,019 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir

2026-06-08 14:57:33,041 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir

2026-06-08 14:57:33,041 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/annot_filter.ok

2026-06-08 14:57:33,043 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 14:57:33,067 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 14:57:33,067 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/EM_adj_counts.ok

2026-06-08 14:57:33,069 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 15:02:26,178 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 4.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 15:02:26,178 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/add_FFPM.ok

2026-06-08 15:02:26,181 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.atNtBlHYmi/fi_workdir/microH.dat

2026-06-08 15:02:26,323 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.atNtBlHYmi/fi_workdir/microH.dat

2026-06-08 15:02:26,323 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/microH.dat.ok

2026-06-08 15:02:26,325 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.atNtBlHYmi/fi_workdir/microH.dat /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 15:02:26,378 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.atNtBlHYmi/fi_workdir/microH.dat /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 15:02:26,378 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/append_microH_info.ok

2026-06-08 15:02:26,380 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv

2026-06-08 15:02:26,382 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv

2026-06-08 15:02:26,382 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_final.ok

2026-06-08 15:02:26,384 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 15:02:26,399 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 15:02:26,399 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/final.abridged.ok

2026-06-08 15:02:26,401 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.atNtBlHYmi --json_outfile /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1

2026-06-08 15:02:26,421 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.atNtBlHYmi --json_outfile /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1

2026-06-08 15:02:26,421 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/create_fi_igvjs.ok

2026-06-08 15:02:26,423 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html

2026-06-08 15:02:27,047 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html

2026-06-08 15:02:27,048 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_reports_html.ok

2026-06-08 15:02:27,050 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 15:02:27,078 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 15:02:27,078 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_annotator.ok

2026-06-08 15:02:27,080 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 15:02:27,146 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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 15:02:27,146 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_coding_region_effect.ok