2026-06-08 10:27:44,479 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:27:51,928 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 BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:27:51,928 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_contigs.ok
2026-06-08 10:27:51,930 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
2026-06-08 10:27:51,932 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
2026-06-08 10:27:51,933 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_contigs_file_workdir
2026-06-08 10:27:51,934 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf
2026-06-08 10:27:51,938 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf
2026-06-08 10:27:51,938 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 10:27:51,939 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/cytoBand.txt
2026-06-08 10:27:52,017 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/cytoBand.txt
2026-06-08 10:27:52,017 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cytoband.ok
2026-06-08 10:27:52,018 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed
2026-06-08 10:27:52,217 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed
2026-06-08 10:27:52,217 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 10:27:52,219 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
2026-06-08 10:27:52,221 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
2026-06-08 10:27:52,222 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.bedsort.ok
2026-06-08 10:27:52,223 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
2026-06-08 10:27:52,231 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed
2026-06-08 10:27:52,231 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.bgzip.ok
2026-06-08 10:27:52,233 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed.gz
2026-06-08 10:27:52,239 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.sorted.bed.gz
2026-06-08 10:27:52,239 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.bed.tabix.ok
2026-06-08 10:27:52,241 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
2026-06-08 10:27:52,249 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa
2026-06-08 10:27:52,250 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/merged_contig_fai.ok
2026-06-08 10:27:52,251 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star --out_dir /tmp/nxf.wrwpEnYaAa/fi_workdir --reads "/tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_2.fastp.fastq.gz"
2026-06-08 11:53:43,707 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 85.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star --out_dir /tmp/nxf.wrwpEnYaAa/fi_workdir --reads "/tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_2.fastp.fastq.gz"
2026-06-08 11:53:43,707 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/run_STAR.ok
2026-06-08 11:53:43,709 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:53:57,864 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:53:57,865 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/mark_dup_reads.ok
2026-06-08 11:53:57,867 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:53:59,632 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:53:59,632 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 11:53:59,634 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:55:40,262 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:55:40,262 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 11:55:40,265 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:59:49,668 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 4.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:59:49,669 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 11:59:49,671 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary
2026-06-08 11:59:49,713 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary
2026-06-08 11:59:49,713 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 11:59:49,715 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:59:49,760 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:59:49,760 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 11:59:49,762 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:59:49,783 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:59:49,783 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 11:59:49,785 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:59:49,801 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:59:49,801 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 11:59:49,803 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam"
2026-06-08 11:59:49,882 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam"
2026-06-08 11:59:49,882 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 11:59:49,884 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam
2026-06-08 11:59:49,895 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam
2026-06-08 11:59:49,895 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 11:59:49,897 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed
2026-06-08 11:59:50,011 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed
2026-06-08 11:59:50,011 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bam_to_bed.ok
2026-06-08 11:59:50,013 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,018 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,018 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bedsort.ok
2026-06-08 11:59:50,020 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,032 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,032 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bgzip.ok
2026-06-08 11:59:50,034 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:59:50,042 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:59:50,042 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.junction_reads.bam.tabix.ok
2026-06-08 11:59:50,044 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:59:50,059 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:59:50,059 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/span_reads_acc.ok
2026-06-08 11:59:50,061 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
2026-06-08 11:59:50,067 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
2026-06-08 11:59:50,068 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 11:59:50,069 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam || :
2026-06-08 11:59:50,109 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam || :
2026-06-08 11:59:50,109 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_spanning_reads.ok
2026-06-08 11:59:50,111 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
2026-06-08 11:59:50,117 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam
2026-06-08 11:59:50,117 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 11:59:50,119 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed
2026-06-08 11:59:50,136 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed
2026-06-08 11:59:50,136 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bam_to_bed.ok
2026-06-08 11:59:50,138 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,140 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,140 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bedsort.ok
2026-06-08 11:59:50,142 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,148 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:59:50,148 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bgzip.ok
2026-06-08 11:59:50,150 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:59:50,156 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:59:50,156 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.spanning_reads.bam.tabix.ok
2026-06-08 11:59:50,158 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
2026-06-08 11:59:50,188 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
2026-06-08 11:59:50,189 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_consol_bam.ok
2026-06-08 11:59:50,191 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
2026-06-08 11:59:51,950 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam
2026-06-08 11:59:51,950 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/index_consol_bam.ok
2026-06-08 11:59:51,953 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 12:00:34,667 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.71 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 12:00:34,667 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 12:00:34,670 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.FusionJuncSpan
2026-06-08 12:00:35,426 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.FusionJuncSpan
2026-06-08 12:00:35,426 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 12:00:35,429 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.gff3
2026-06-08 12:00:35,536 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.gff3
2026-06-08 12:00:35,536 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 12:00:35,538 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.bed
2026-06-08 12:00:35,592 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.Pfam.bed
2026-06-08 12:00:35,592 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 12:00:35,594 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.gff3
2026-06-08 12:00:35,636 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.gff3
2026-06-08 12:00:35,637 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 12:00:35,639 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.bed
2026-06-08 12:00:35,660 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.igv.seqsimilar.bed
2026-06-08 12:00:35,660 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 12:00:35,662 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 12:00:35,727 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa > /tmp/nxf.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 12:00:35,728 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/add_splice_info.ok
2026-06-08 12:00:35,730 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 12:00:35,885 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.wrwpEnYaAa/fi_workdir/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 12:00:35,886 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/blast_filter.ok
2026-06-08 12:00:35,887 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir
2026-06-08 12:00:35,907 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir
2026-06-08 12:00:35,908 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/annot_filter.ok
2026-06-08 12:00:35,909 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 12:00:35,937 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 12:00:35,937 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/EM_adj_counts.ok
2026-06-08 12:00:35,939 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:06:18,879 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.72 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:06:18,880 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/add_FFPM.ok
2026-06-08 12:06:18,882 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --gtf /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/fi_workdir/microH.dat
2026-06-08 12:06:19,118 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fa --gtf /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.gtf > /tmp/nxf.wrwpEnYaAa/fi_workdir/microH.dat
2026-06-08 12:06:19,118 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/microH.dat.ok
2026-06-08 12:06:19,120 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.wrwpEnYaAa/fi_workdir/microH.dat /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:06:19,158 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.wrwpEnYaAa/fi_workdir/microH.dat /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:06:19,158 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/append_microH_info.ok
2026-06-08 12:06:19,161 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv
2026-06-08 12:06:19,163 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv
2026-06-08 12:06:19,163 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/cp_final.ok
2026-06-08 12:06:19,165 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:06:19,180 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:06:19,181 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/final.abridged.ok
2026-06-08 12:06:19,182 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.wrwpEnYaAa --json_outfile /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1
2026-06-08 12:06:19,203 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.wrwpEnYaAa --json_outfile /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1
2026-06-08 12:06:19,203 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/create_fi_igvjs.ok
2026-06-08 12:06:19,205 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --html_output /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.html
2026-06-08 12:06:20,191 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 --html_output /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.fusion_inspector_web.html
2026-06-08 12:06:20,191 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_reports_html.ok
2026-06-08 12:06:20,193 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:06:20,225 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:06:20,225 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_annotator.ok
2026-06-08 12:06:20,227 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:06:20,298 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.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.wrwpEnYaAa/ctat_genome_lib_build_dir > /tmp/nxf.wrwpEnYaAa/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:06:20,298 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.wrwpEnYaAa/chckpts_dir/fusion_coding_region_effect.ok