2026-06-03 21:09:19,709 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 2026-06-03 21:09:27,686 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 2026-06-03 21:09:27,686 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/fusion_contigs.ok 2026-06-03 21:09:27,688 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa 2026-06-03 21:09:27,691 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa 2026-06-03 21:09:27,691 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/cp_contigs_file_workdir 2026-06-03 21:09:27,693 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf 2026-06-03 21:09:27,699 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf 2026-06-03 21:09:27,699 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/cp_gtf_file_workdir.ok 2026-06-03 21:09:27,700 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf > /tmp/nxf.U2E8LSePa5/cytoBand.txt 2026-06-03 21:09:27,835 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf > /tmp/nxf.U2E8LSePa5/cytoBand.txt 2026-06-03 21:09:27,836 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/cytoband.ok 2026-06-03 21:09:27,838 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed 2026-06-03 21:09:28,218 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed 2026-06-03 21:09:28,218 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/merged_contig_gtf_to_bed.ok 2026-06-03 21:09:28,220 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.sorted.bed 2026-06-03 21:09:28,223 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.sorted.bed 2026-06-03 21:09:28,223 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.bedsort.ok 2026-06-03 21:09:28,225 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.sorted.bed 2026-06-03 21:09:28,237 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.sorted.bed 2026-06-03 21:09:28,237 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.bgzip.ok 2026-06-03 21:09:28,239 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.sorted.bed.gz 2026-06-03 21:09:28,246 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.sorted.bed.gz 2026-06-03 21:09:28,246 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.bed.tabix.ok 2026-06-03 21:09:28,248 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools faidx /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa 2026-06-03 21:09:28,260 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa 2026-06-03 21:09:28,260 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/merged_contig_fai.ok 2026-06-03 21:09:28,262 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --CPU 8 --out_prefix FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star --out_dir /tmp/nxf.U2E8LSePa5/fi_workdir --reads "/tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_2.fastp.fastq.gz" 2026-06-03 22:24:23,704 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 74.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --CPU 8 --out_prefix FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star --out_dir /tmp/nxf.U2E8LSePa5/fi_workdir --reads "/tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_2.fastp.fastq.gz" 2026-06-03 22:24:23,704 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/run_STAR.ok 2026-06-03 22:24:23,706 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-03 22:24:51,430 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-03 22:24:51,430 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/mark_dup_reads.ok 2026-06-03 22:24:51,432 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam 2026-06-03 22:24:54,744 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam 2026-06-03 22:24:54,744 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/mark_dups_reads.index.ok 2026-06-03 22:24:54,746 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-03 22:27:38,696 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 2.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-03 22:27:38,696 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 2026-06-03 22:27:38,698 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-03 22:35:31,607 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 7.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-03 22:35:31,607 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 2026-06-03 22:35:31,609 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary 2026-06-03 22:35:31,776 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary 2026-06-03 22:35:31,776 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/coalesce_junc_n_span.ok 2026-06-03 22:35:31,778 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-03 22:35:32,050 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-03 22:35:32,050 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/init_EM_adj_counts.ok 2026-06-03 22:35:32,052 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-03 22:35:32,080 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-03 22:35:32,081 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/filter_by_frag_threshs.ok 2026-06-03 22:35:32,082 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-03 22:35:32,102 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-03 22:35:32,102 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_extract_junc_reads.ok 2026-06-03 22:35:32,104 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam" 2026-06-03 22:35:32,246 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam" 2026-06-03 22:35:32,247 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_junc_reads_bam.ok 2026-06-03 22:35:32,248 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam 2026-06-03 22:35:32,265 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam 2026-06-03 22:35:32,265 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/samtools_idx_junc_reads_bam.ok 2026-06-03 22:35:32,266 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed 2026-06-03 22:35:32,584 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed 2026-06-03 22:35:32,585 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok 2026-06-03 22:35:32,586 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,595 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,596 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bedsort.ok 2026-06-03 22:35:32,597 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,622 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,622 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bgzip.ok 2026-06-03 22:35:32,624 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-03 22:35:32,633 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-03 22:35:32,633 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.junction_reads.bam.tabix.ok 2026-06-03 22:35:32,635 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-03 22:35:32,655 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-03 22:35:32,655 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/span_reads_acc.ok 2026-06-03 22:35:32,657 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools view -H /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam 2026-06-03 22:35:32,662 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam 2026-06-03 22:35:32,662 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/init_spanning_reads_bam.ok 2026-06-03 22:35:32,664 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam || : 2026-06-03 22:35:32,705 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam || : 2026-06-03 22:35:32,705 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_spanning_reads.ok 2026-06-03 22:35:32,707 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam 2026-06-03 22:35:32,712 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam 2026-06-03 22:35:32,712 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/samtools_index_span_reads_bam.ok 2026-06-03 22:35:32,714 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed 2026-06-03 22:35:32,737 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed 2026-06-03 22:35:32,737 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok 2026-06-03 22:35:32,738 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,740 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,740 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok 2026-06-03 22:35:32,742 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,747 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-03 22:35:32,747 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok 2026-06-03 22:35:32,749 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-03 22:35:32,754 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-03 22:35:32,754 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.spanning_reads.bam.tabix.ok 2026-06-03 22:35:32,756 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam 2026-06-03 22:35:32,808 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam 2026-06-03 22:35:32,808 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/cp_consol_bam.ok 2026-06-03 22:35:32,809 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam 2026-06-03 22:35:36,092 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam 2026-06-03 22:35:36,092 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/index_consol_bam.ok 2026-06-03 22:35:36,094 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 2026-06-03 22:36:51,608 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 2026-06-03 22:36:51,608 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_sam_frag_coordss.ok 2026-06-03 22:36:51,611 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.FusionJuncSpan 2026-06-03 22:36:52,883 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.FusionJuncSpan 2026-06-03 22:36:52,883 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_juncspan_fmt.ok 2026-06-03 22:36:52,885 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.Pfam.gff3 2026-06-03 22:36:53,115 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.Pfam.gff3 2026-06-03 22:36:53,115 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_pfam_gff3.ok 2026-06-03 22:36:53,117 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.Pfam.bed 2026-06-03 22:36:53,218 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.Pfam.bed 2026-06-03 22:36:53,218 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_pfam_bed.ok 2026-06-03 22:36:53,219 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.seqsimilar.gff3 2026-06-03 22:36:53,280 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.seqsimilar.gff3 2026-06-03 22:36:53,280 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_seqsim_gff3.ok 2026-06-03 22:36:53,282 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.seqsimilar.bed 2026-06-03 22:36:53,303 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.igv.seqsimilar.bed 2026-06-03 22:36:53,303 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/prep_igv_seqsim_bed.ok 2026-06-03 22:36:53,305 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-03 22:36:53,410 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa > /tmp/nxf.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-03 22:36:53,410 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/add_splice_info.ok 2026-06-03 22:36:53,412 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-03 22:36:53,586 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.U2E8LSePa5/fi_workdir/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-03 22:36:53,586 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/blast_filter.ok 2026-06-03 22:36:53,588 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir 2026-06-03 22:36:53,614 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir 2026-06-03 22:36:53,614 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/annot_filter.ok 2026-06-03 22:36:53,616 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-03 22:36:53,668 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-03 22:36:53,668 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/EM_adj_counts.ok 2026-06-03 22:36:53,670 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-03 22:42:51,945 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 5.97 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-03 22:42:51,945 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/add_FFPM.ok 2026-06-03 22:42:51,947 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa --gtf /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf > /tmp/nxf.U2E8LSePa5/fi_workdir/microH.dat 2026-06-03 22:42:52,400 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fa --gtf /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.gtf > /tmp/nxf.U2E8LSePa5/fi_workdir/microH.dat 2026-06-03 22:42:52,400 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/microH.dat.ok 2026-06-03 22:42:52,402 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.U2E8LSePa5/fi_workdir/microH.dat /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-03 22:42:52,544 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.U2E8LSePa5/fi_workdir/microH.dat /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-03 22:42:52,544 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/append_microH_info.ok 2026-06-03 22:42:52,546 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.tsv 2026-06-03 22:42:52,549 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.tsv 2026-06-03 22:42:52,550 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/cp_final.ok 2026-06-03 22:42:52,551 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv 2026-06-03 22:42:52,570 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv 2026-06-03 22:42:52,570 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/final.abridged.ok 2026-06-03 22:42:52,572 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.U2E8LSePa5 --json_outfile /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix FFPE_HD789_01_RNA_13_A23YTGFLT4_1 2026-06-03 22:42:52,593 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.U2E8LSePa5 --json_outfile /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix FFPE_HD789_01_RNA_13_A23YTGFLT4_1 2026-06-03 22:42:52,593 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/create_fi_igvjs.ok 2026-06-03 22:42:52,595 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix FFPE_HD789_01_RNA_13_A23YTGFLT4_1 --html_output /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_inspector_web.html 2026-06-03 22:42:54,343 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.03 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix FFPE_HD789_01_RNA_13_A23YTGFLT4_1 --html_output /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.fusion_inspector_web.html 2026-06-03 22:42:54,344 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/fusion_reports_html.ok 2026-06-03 22:42:54,345 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-03 22:42:54,383 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-03 22:42:54,383 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/fusion_annotator.ok 2026-06-03 22:42:54,385 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-03 22:42:54,660 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.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.U2E8LSePa5/ctat_genome_lib_build_dir > /tmp/nxf.U2E8LSePa5/FFPE_HD789_01_RNA_13_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-03 22:42:54,661 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.U2E8LSePa5/chckpts_dir/fusion_coding_region_effect.ok