2026-06-08 10:20:03,468 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 2026-06-08 10:20:10,386 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_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 2026-06-08 10:20:10,386 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/fusion_contigs.ok 2026-06-08 10:20:10,388 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:20:10,391 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:20:10,391 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/cp_contigs_file_workdir 2026-06-08 10:20:10,392 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf 2026-06-08 10:20:10,394 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf 2026-06-08 10:20:10,395 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/cp_gtf_file_workdir.ok 2026-06-08 10:20:10,396 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4cFDybVH2L/cytoBand.txt 2026-06-08 10:20:10,428 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4cFDybVH2L/cytoBand.txt 2026-06-08 10:20:10,428 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/cytoband.ok 2026-06-08 10:20:10,429 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed 2026-06-08 10:20:10,524 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed 2026-06-08 10:20:10,524 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/merged_contig_gtf_to_bed.ok 2026-06-08 10:20:10,525 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:20:10,527 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:20:10,527 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok 2026-06-08 10:20:10,529 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:20:10,534 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:20:10,535 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok 2026-06-08 10:20:10,536 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz 2026-06-08 10:20:10,541 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz 2026-06-08 10:20:10,541 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok 2026-06-08 10:20:10,543 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools faidx /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:20:10,549 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:20:10,549 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/merged_contig_fai.ok 2026-06-08 10:20:10,550 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.4cFDybVH2L/fi_workdir --reads "/tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" 2026-06-08 11:18:31,278 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 58.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.4cFDybVH2L/fi_workdir --reads "/tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" 2026-06-08 11:18:31,278 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/run_STAR.ok 2026-06-08 11:18:31,281 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 11:18:33,381 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 11:18:33,381 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/mark_dup_reads.ok 2026-06-08 11:18:33,383 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam 2026-06-08 11:18:33,651 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam 2026-06-08 11:18:33,652 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/mark_dups_reads.index.ok 2026-06-08 11:18:33,654 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 11:18:47,878 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 11:18:47,878 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 2026-06-08 11:18:47,880 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 11:19:27,364 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 11:19:27,364 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 2026-06-08 11:19:27,367 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary 2026-06-08 11:19:27,382 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary 2026-06-08 11:19:27,383 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/coalesce_junc_n_span.ok 2026-06-08 11:19:27,384 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-08 11:19:27,400 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-08 11:19:27,400 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/init_EM_adj_counts.ok 2026-06-08 11:19:27,402 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 11:19:27,419 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 11:19:27,419 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/filter_by_frag_threshs.ok 2026-06-08 11:19:27,421 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 11:19:27,434 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 11:19:27,434 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_extract_junc_reads.ok 2026-06-08 11:19:27,436 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" 2026-06-08 11:19:27,491 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" 2026-06-08 11:19:27,491 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_junc_reads_bam.ok 2026-06-08 11:19:27,492 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam 2026-06-08 11:19:27,498 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam 2026-06-08 11:19:27,498 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/samtools_idx_junc_reads_bam.ok 2026-06-08 11:19:27,500 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed 2026-06-08 11:19:27,538 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed 2026-06-08 11:19:27,538 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok 2026-06-08 11:19:27,540 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,542 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,542 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok 2026-06-08 11:19:27,544 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,550 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,550 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok 2026-06-08 11:19:27,552 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 11:19:27,557 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 11:19:27,557 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok 2026-06-08 11:19:27,559 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 11:19:27,572 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 11:19:27,572 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/span_reads_acc.ok 2026-06-08 11:19:27,574 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools view -H /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:19:27,579 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:19:27,579 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/init_spanning_reads_bam.ok 2026-06-08 11:19:27,580 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 2026-06-08 11:19:27,596 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 2026-06-08 11:19:27,596 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_spanning_reads.ok 2026-06-08 11:19:27,598 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:19:27,602 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:19:27,602 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/samtools_index_span_reads_bam.ok 2026-06-08 11:19:27,603 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed 2026-06-08 11:19:27,618 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed 2026-06-08 11:19:27,618 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok 2026-06-08 11:19:27,620 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,621 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,621 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok 2026-06-08 11:19:27,623 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,628 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:19:27,628 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok 2026-06-08 11:19:27,629 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 11:19:27,634 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 11:19:27,634 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok 2026-06-08 11:19:27,636 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:19:27,642 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:19:27,642 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/cp_consol_bam.ok 2026-06-08 11:19:27,643 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:19:27,910 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:19:27,910 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/index_consol_bam.ok 2026-06-08 11:19:27,912 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 2026-06-08 11:19:35,284 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 2026-06-08 11:19:35,284 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_sam_frag_coordss.ok 2026-06-08 11:19:35,286 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan 2026-06-08 11:19:35,443 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan 2026-06-08 11:19:35,444 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_juncspan_fmt.ok 2026-06-08 11:19:35,445 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 2026-06-08 11:19:35,502 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 2026-06-08 11:19:35,502 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_pfam_gff3.ok 2026-06-08 11:19:35,504 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed 2026-06-08 11:19:35,543 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed 2026-06-08 11:19:35,543 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_pfam_bed.ok 2026-06-08 11:19:35,544 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 2026-06-08 11:19:35,572 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 2026-06-08 11:19:35,572 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_seqsim_gff3.ok 2026-06-08 11:19:35,574 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed 2026-06-08 11:19:35,594 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed 2026-06-08 11:19:35,594 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/prep_igv_seqsim_bed.ok 2026-06-08 11:19:35,595 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 11:19:35,623 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 11:19:35,623 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/add_splice_info.ok 2026-06-08 11:19:35,624 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4cFDybVH2L/1173_RQT_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 11:19:35,768 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.4cFDybVH2L/fi_workdir/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4cFDybVH2L/1173_RQT_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 11:19:35,768 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/blast_filter.ok 2026-06-08 11:19:35,770 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir 2026-06-08 11:19:35,788 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir 2026-06-08 11:19:35,788 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/annot_filter.ok 2026-06-08 11:19:35,790 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 11:19:35,805 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 11:19:35,805 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/EM_adj_counts.ok 2026-06-08 11:19:35,807 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 11:24:05,967 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 4.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 11:24:05,967 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/add_FFPM.ok 2026-06-08 11:24:05,969 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4cFDybVH2L/fi_workdir/microH.dat 2026-06-08 11:24:06,045 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4cFDybVH2L/fi_workdir/microH.dat 2026-06-08 11:24:06,045 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/microH.dat.ok 2026-06-08 11:24:06,047 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.4cFDybVH2L/fi_workdir/microH.dat /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 11:24:06,064 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.4cFDybVH2L/fi_workdir/microH.dat /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 11:24:06,065 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/append_microH_info.ok 2026-06-08 11:24:06,066 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv 2026-06-08 11:24:06,068 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv 2026-06-08 11:24:06,068 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/cp_final.ok 2026-06-08 11:24:06,070 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv 2026-06-08 11:24:06,082 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv 2026-06-08 11:24:06,083 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/final.abridged.ok 2026-06-08 11:24:06,084 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.4cFDybVH2L --json_outfile /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1 2026-06-08 11:24:06,104 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.4cFDybVH2L --json_outfile /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1 2026-06-08 11:24:06,104 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/create_fi_igvjs.ok 2026-06-08 11:24:06,105 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html 2026-06-08 11:24:06,455 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html 2026-06-08 11:24:06,455 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/fusion_reports_html.ok 2026-06-08 11:24:06,457 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 11:24:06,481 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 11:24:06,481 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/fusion_annotator.ok 2026-06-08 11:24:06,483 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 11:24:06,530 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.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4cFDybVH2L/ctat_genome_lib_build_dir > /tmp/nxf.4cFDybVH2L/1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 11:24:06,530 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.4cFDybVH2L/chckpts_dir/fusion_coding_region_effect.ok