2026-06-03 20:23:20,434 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
2026-06-03 20:23:28,248 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 aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000
2026-06-03 20:23:28,248 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_contigs.ok
2026-06-03 20:23:28,250 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
2026-06-03 20:23:28,253 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
2026-06-03 20:23:28,253 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_contigs_file_workdir
2026-06-03 20:23:28,255 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
2026-06-03 20:23:28,259 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf
2026-06-03 20:23:28,259 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-03 20:23:28,261 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/cytoBand.txt
2026-06-03 20:23:28,394 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/cytoBand.txt
2026-06-03 20:23:28,395 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cytoband.ok
2026-06-03 20:23:28,396 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed
2026-06-03 20:23:28,776 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed
2026-06-03 20:23:28,776 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-03 20:23:28,778 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
2026-06-03 20:23:28,780 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
2026-06-03 20:23:28,780 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.bedsort.ok
2026-06-03 20:23:28,781 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
2026-06-03 20:23:28,792 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed
2026-06-03 20:23:28,792 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.bgzip.ok
2026-06-03 20:23:28,794 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed.gz
2026-06-03 20:23:28,800 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed.gz
2026-06-03 20:23:28,801 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.tabix.ok
2026-06-03 20:23:28,802 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
2026-06-03 20:23:28,814 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa
2026-06-03 20:23:28,814 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/merged_contig_fai.ok
2026-06-03 20:23:28,815 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.4vpUnjdFeW/fi_workdir --reads "/tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
2026-06-03 21:00:05,212 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 36.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.4vpUnjdFeW/fi_workdir --reads "/tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz"
2026-06-03 21:00:05,212 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/run_STAR.ok
2026-06-03 21:00:05,214 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-03 21:00:27,427 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-03 21:00:27,428 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/mark_dup_reads.ok
2026-06-03 21:00:27,430 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
2026-06-03 21:00:30,166 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
2026-06-03 21:00:30,166 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/mark_dups_reads.index.ok
2026-06-03 21:00:30,168 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-03 21:02:46,582 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 2.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-03 21:02:46,583 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-03 21:02:46,585 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-03 21:09:35,685 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 6.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-03 21:09:35,685 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-03 21:09:35,687 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
2026-06-03 21:09:35,757 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary
2026-06-03 21:09:35,757 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/coalesce_junc_n_span.ok
2026-06-03 21:09:35,759 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-03 21:09:35,938 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-03 21:09:35,938 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/init_EM_adj_counts.ok
2026-06-03 21:09:35,940 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-03 21:09:35,962 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-03 21:09:35,962 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/filter_by_frag_threshs.ok
2026-06-03 21:09:35,964 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-03 21:09:35,979 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-03 21:09:35,979 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-03 21:09:35,981 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam"
2026-06-03 21:09:36,080 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam"
2026-06-03 21:09:36,080 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-03 21:09:36,081 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam
2026-06-03 21:09:36,093 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam
2026-06-03 21:09:36,093 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-03 21:09:36,094 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed
2026-06-03 21:09:36,270 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed
2026-06-03 21:09:36,270 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok
2026-06-03 21:09:36,272 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,277 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,277 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok
2026-06-03 21:09:36,278 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,295 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,295 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok
2026-06-03 21:09:36,297 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-03 21:09:36,304 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-03 21:09:36,304 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok
2026-06-03 21:09:36,305 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-03 21:09:36,320 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-03 21:09:36,320 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/span_reads_acc.ok
2026-06-03 21:09:36,322 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
2026-06-03 21:09:36,327 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
2026-06-03 21:09:36,327 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/init_spanning_reads_bam.ok
2026-06-03 21:09:36,329 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam || :
2026-06-03 21:09:36,364 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam || :
2026-06-03 21:09:36,365 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_spanning_reads.ok
2026-06-03 21:09:36,366 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
2026-06-03 21:09:36,371 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam
2026-06-03 21:09:36,371 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-03 21:09:36,372 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed
2026-06-03 21:09:36,389 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed
2026-06-03 21:09:36,389 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok
2026-06-03 21:09:36,390 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,392 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,392 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok
2026-06-03 21:09:36,394 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,399 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-03 21:09:36,399 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok
2026-06-03 21:09:36,400 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-03 21:09:36,405 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-03 21:09:36,405 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok
2026-06-03 21:09:36,406 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
2026-06-03 21:09:36,449 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
2026-06-03 21:09:36,449 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_consol_bam.ok
2026-06-03 21:09:36,450 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
2026-06-03 21:09:39,179 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam
2026-06-03 21:09:39,179 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/index_consol_bam.ok
2026-06-03 21:09:39,181 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
2026-06-03 21:10:41,525 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000
2026-06-03 21:10:41,525 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-03 21:10:41,527 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.FusionJuncSpan
2026-06-03 21:10:42,636 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.FusionJuncSpan
2026-06-03 21:10:42,636 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-03 21:10:42,638 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3
2026-06-03 21:10:42,858 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3
2026-06-03 21:10:42,858 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-03 21:10:42,860 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.bed
2026-06-03 21:10:42,963 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.bed
2026-06-03 21:10:42,963 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-03 21:10:42,965 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
2026-06-03 21:10:43,028 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3
2026-06-03 21:10:43,028 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-03 21:10:43,029 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.bed
2026-06-03 21:10:43,050 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.bed
2026-06-03 21:10:43,051 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-03 21:10:43,052 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-03 21:10:43,153 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-03 21:10:43,153 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/add_splice_info.ok
2026-06-03 21:10:43,155 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-03 21:10:43,314 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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-03 21:10:43,314 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/blast_filter.ok
2026-06-03 21:10:43,315 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir
2026-06-03 21:10:43,336 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir
2026-06-03 21:10:43,336 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/annot_filter.ok
2026-06-03 21:10:43,337 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-03 21:10:43,366 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-03 21:10:43,366 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/EM_adj_counts.ok
2026-06-03 21:10:43,368 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-03 21:13:46,717 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 3.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-03 21:13:46,717 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/add_FFPM.ok
2026-06-03 21:13:46,719 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat
2026-06-03 21:13:47,180 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat
2026-06-03 21:13:47,180 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/microH.dat.ok
2026-06-03 21:13:47,182 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-03 21:13:47,250 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.4vpUnjdFeW/fi_workdir/microH.dat /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-03 21:13:47,250 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/append_microH_info.ok
2026-06-03 21:13:47,251 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
2026-06-03 21:13:47,253 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv
2026-06-03 21:13:47,254 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_final.ok
2026-06-03 21:13:47,255 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
2026-06-03 21:13:47,270 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv
2026-06-03 21:13:47,270 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/final.abridged.ok
2026-06-03 21:13:47,272 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.4vpUnjdFeW --json_outfile /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1
2026-06-03 21:13:47,292 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.4vpUnjdFeW --json_outfile /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1
2026-06-03 21:13:47,292 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/create_fi_igvjs.ok
2026-06-03 21:13:47,294 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --html_output /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.html
2026-06-03 21:13:49,018 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --html_output /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.html
2026-06-03 21:13:49,018 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_reports_html.ok
2026-06-03 21:13:49,020 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-03 21:13:49,055 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-03 21:13:49,056 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_annotator.ok
2026-06-03 21:13:49,057 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-03 21:13:49,199 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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-03 21:13:49,199 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_coding_region_effect.ok