2026-06-08 10:28:24,636 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00676_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 2026-06-08 10:28:32,547 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 tih_rna_sample_00676_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 2026-06-08 10:28:32,547 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/fusion_contigs.ok 2026-06-08 10:28:32,549 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fa 2026-06-08 10:28:32,552 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fa 2026-06-08 10:28:32,552 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/cp_contigs_file_workdir 2026-06-08 10:28:32,554 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf 2026-06-08 10:28:32,558 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf 2026-06-08 10:28:32,558 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/cp_gtf_file_workdir.ok 2026-06-08 10:28:32,559 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf > /tmp/nxf.RoPOUI5bJu/cytoBand.txt 2026-06-08 10:28:32,650 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf > /tmp/nxf.RoPOUI5bJu/cytoBand.txt 2026-06-08 10:28:32,650 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/cytoband.ok 2026-06-08 10:28:32,652 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed 2026-06-08 10:28:32,893 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed 2026-06-08 10:28:32,894 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/merged_contig_gtf_to_bed.ok 2026-06-08 10:28:32,896 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed.sorted.bed 2026-06-08 10:28:32,898 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed.sorted.bed 2026-06-08 10:28:32,898 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.bed.bedsort.ok 2026-06-08 10:28:32,900 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed.sorted.bed 2026-06-08 10:28:32,916 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed.sorted.bed 2026-06-08 10:28:32,916 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.bed.bgzip.ok 2026-06-08 10:28:32,918 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed.sorted.bed.gz 2026-06-08 10:28:32,925 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.bed.sorted.bed.gz 2026-06-08 10:28:32,925 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.bed.tabix.ok 2026-06-08 10:28:32,926 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools faidx /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa 2026-06-08 10:28:32,939 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa 2026-06-08 10:28:32,939 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/merged_contig_fai.ok 2026-06-08 10:28:32,941 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00676_B23MVV7LT4_1.star --out_dir /tmp/nxf.RoPOUI5bJu/fi_workdir --reads "/tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1_2.fastp.fastq.gz" 2026-06-08 12:03:21,190 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 94.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00676_B23MVV7LT4_1.star --out_dir /tmp/nxf.RoPOUI5bJu/fi_workdir --reads "/tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1_2.fastp.fastq.gz" 2026-06-08 12:03:21,190 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/run_STAR.ok 2026-06-08 12:03:21,192 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 12:03:39,071 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 12:03:39,072 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/mark_dup_reads.ok 2026-06-08 12:03:39,074 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam 2026-06-08 12:03:41,256 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam 2026-06-08 12:03:41,256 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/mark_dups_reads.index.ok 2026-06-08 12:03:41,259 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 12:05:33,346 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 1.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 12:05:33,346 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 2026-06-08 12:05:33,348 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 12:10:40,202 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 5.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 12:10:40,203 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 2026-06-08 12:10:40,205 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary 2026-06-08 12:10:40,408 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary 2026-06-08 12:10:40,409 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/coalesce_junc_n_span.ok 2026-06-08 12:10:40,410 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-08 12:10:40,483 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-08 12:10:40,483 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/init_EM_adj_counts.ok 2026-06-08 12:10:40,485 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 12:10:40,514 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 12:10:40,514 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/filter_by_frag_threshs.ok 2026-06-08 12:10:40,516 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 12:10:40,537 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 12:10:40,538 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_extract_junc_reads.ok 2026-06-08 12:10:40,539 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam" 2026-06-08 12:10:40,694 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam" 2026-06-08 12:10:40,694 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_junc_reads_bam.ok 2026-06-08 12:10:40,696 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam 2026-06-08 12:10:40,713 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam 2026-06-08 12:10:40,714 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/samtools_idx_junc_reads_bam.ok 2026-06-08 12:10:40,715 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed 2026-06-08 12:10:41,054 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed 2026-06-08 12:10:41,055 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok 2026-06-08 12:10:41,057 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,066 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,067 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bedsort.ok 2026-06-08 12:10:41,068 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,096 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,096 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bgzip.ok 2026-06-08 12:10:41,098 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 12:10:41,109 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 12:10:41,109 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.junction_reads.bam.tabix.ok 2026-06-08 12:10:41,110 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 12:10:41,131 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 12:10:41,131 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/span_reads_acc.ok 2026-06-08 12:10:41,133 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools view -H /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam 2026-06-08 12:10:41,138 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam 2026-06-08 12:10:41,139 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/init_spanning_reads_bam.ok 2026-06-08 12:10:41,140 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam || : 2026-06-08 12:10:41,194 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam || : 2026-06-08 12:10:41,194 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_spanning_reads.ok 2026-06-08 12:10:41,195 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam 2026-06-08 12:10:41,201 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam 2026-06-08 12:10:41,201 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/samtools_index_span_reads_bam.ok 2026-06-08 12:10:41,203 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed 2026-06-08 12:10:41,230 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed 2026-06-08 12:10:41,230 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok 2026-06-08 12:10:41,232 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,234 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,234 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok 2026-06-08 12:10:41,236 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,242 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 12:10:41,242 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok 2026-06-08 12:10:41,244 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 12:10:41,250 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 12:10:41,250 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/tih_rna_sample_00676_B23MVV7LT4_1.spanning_reads.bam.tabix.ok 2026-06-08 12:10:41,251 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam 2026-06-08 12:10:41,287 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam 2026-06-08 12:10:41,287 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/cp_consol_bam.ok 2026-06-08 12:10:41,289 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam 2026-06-08 12:10:43,480 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam 2026-06-08 12:10:43,481 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/index_consol_bam.ok 2026-06-08 12:10:43,483 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 2026-06-08 12:11:34,876 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 2026-06-08 12:11:34,876 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_sam_frag_coordss.ok 2026-06-08 12:11:34,878 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.FusionJuncSpan 2026-06-08 12:11:35,790 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.FusionJuncSpan 2026-06-08 12:11:35,790 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_juncspan_fmt.ok 2026-06-08 12:11:35,792 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.Pfam.gff3 2026-06-08 12:11:35,904 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.Pfam.gff3 2026-06-08 12:11:35,904 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_pfam_gff3.ok 2026-06-08 12:11:35,906 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.Pfam.bed 2026-06-08 12:11:35,951 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.Pfam.bed 2026-06-08 12:11:35,951 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_pfam_bed.ok 2026-06-08 12:11:35,952 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.seqsimilar.gff3 2026-06-08 12:11:35,999 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.seqsimilar.gff3 2026-06-08 12:11:35,999 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_seqsim_gff3.ok 2026-06-08 12:11:36,001 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.seqsimilar.bed 2026-06-08 12:11:36,022 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.igv.seqsimilar.bed 2026-06-08 12:11:36,022 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/prep_igv_seqsim_bed.ok 2026-06-08 12:11:36,024 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 12:11:36,101 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa > /tmp/nxf.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 12:11:36,101 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/add_splice_info.ok 2026-06-08 12:11:36,103 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-08 12:11:36,278 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.RoPOUI5bJu/fi_workdir/tih_rna_sample_00676_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-08 12:11:36,278 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/blast_filter.ok 2026-06-08 12:11:36,280 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir 2026-06-08 12:11:36,306 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir 2026-06-08 12:11:36,306 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/annot_filter.ok 2026-06-08 12:11:36,308 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 12:11:36,365 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 12:11:36,365 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/EM_adj_counts.ok 2026-06-08 12:11:36,367 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 12:17:24,553 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 5.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 12:17:24,553 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/add_FFPM.ok 2026-06-08 12:17:24,556 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa --gtf /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf > /tmp/nxf.RoPOUI5bJu/fi_workdir/microH.dat 2026-06-08 12:17:24,838 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fa --gtf /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.gtf > /tmp/nxf.RoPOUI5bJu/fi_workdir/microH.dat 2026-06-08 12:17:24,838 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/microH.dat.ok 2026-06-08 12:17:24,840 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.RoPOUI5bJu/fi_workdir/microH.dat /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 12:17:24,962 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.RoPOUI5bJu/fi_workdir/microH.dat /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 12:17:24,962 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/append_microH_info.ok 2026-06-08 12:17:24,964 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.tsv 2026-06-08 12:17:24,968 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.tsv 2026-06-08 12:17:24,968 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/cp_final.ok 2026-06-08 12:17:24,970 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv 2026-06-08 12:17:24,989 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv 2026-06-08 12:17:24,989 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/final.abridged.ok 2026-06-08 12:17:24,990 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.RoPOUI5bJu --json_outfile /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00676_B23MVV7LT4_1 2026-06-08 12:17:25,011 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.RoPOUI5bJu --json_outfile /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00676_B23MVV7LT4_1 2026-06-08 12:17:25,011 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/create_fi_igvjs.ok 2026-06-08 12:17:25,013 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00676_B23MVV7LT4_1 --html_output /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fusion_inspector_web.html 2026-06-08 12:17:26,285 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00676_B23MVV7LT4_1 --html_output /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.fusion_inspector_web.html 2026-06-08 12:17:26,285 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/fusion_reports_html.ok 2026-06-08 12:17:26,287 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 12:17:26,317 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 12:17:26,317 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/fusion_annotator.ok 2026-06-08 12:17:26,319 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 12:17:26,452 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.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.RoPOUI5bJu/ctat_genome_lib_build_dir > /tmp/nxf.RoPOUI5bJu/tih_rna_sample_00676_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 12:17:26,452 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.RoPOUI5bJu/chckpts_dir/fusion_coding_region_effect.ok