2026-03-03 19:17:23,445 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LVxD8jMVWP/rna_s1221_S42 --shrink_introns --max_intron_length 1000 2026-03-03 19:17:33,112 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LVxD8jMVWP/rna_s1221_S42 --shrink_introns --max_intron_length 1000 2026-03-03 19:17:33,112 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/fusion_contigs.ok 2026-03-03 19:17:33,114 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fa 2026-03-03 19:17:33,116 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fa 2026-03-03 19:17:33,116 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/cp_contigs_file_workdir 2026-03-03 19:17:33,118 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf 2026-03-03 19:17:33,121 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf 2026-03-03 19:17:33,121 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/cp_gtf_file_workdir.ok 2026-03-03 19:17:33,122 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf > /tmp/nxf.LVxD8jMVWP/cytoBand.txt 2026-03-03 19:17:33,187 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.LVxD8jMVWP/rna_s1221_S42.fa /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf > /tmp/nxf.LVxD8jMVWP/cytoBand.txt 2026-03-03 19:17:33,187 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/cytoband.ok 2026-03-03 19:17:33,188 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed 2026-03-03 19:17:33,369 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.LVxD8jMVWP/rna_s1221_S42.gtf > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed 2026-03-03 19:17:33,369 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/merged_contig_gtf_to_bed.ok 2026-03-03 19:17:33,371 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed.sorted.bed 2026-03-03 19:17:33,374 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed.sorted.bed 2026-03-03 19:17:33,374 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.bed.bedsort.ok 2026-03-03 19:17:33,376 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed.sorted.bed 2026-03-03 19:17:33,383 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed.sorted.bed 2026-03-03 19:17:33,383 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.bed.bgzip.ok 2026-03-03 19:17:33,385 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed.sorted.bed.gz 2026-03-03 19:17:33,390 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.bed.sorted.bed.gz 2026-03-03 19:17:33,390 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.bed.tabix.ok 2026-03-03 19:17:33,392 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools faidx /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa 2026-03-03 19:17:33,399 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa 2026-03-03 19:17:33,399 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/merged_contig_fai.ok 2026-03-03 19:17:33,401 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.LVxD8jMVWP/fi_workdir --reads "/tmp/nxf.LVxD8jMVWP/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.LVxD8jMVWP/rna_s1221_S42_2.fastp.fastq.gz" 2026-03-03 19:25:30,275 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 7.95 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.LVxD8jMVWP/fi_workdir --reads "/tmp/nxf.LVxD8jMVWP/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.LVxD8jMVWP/rna_s1221_S42_2.fastp.fastq.gz" 2026-03-03 19:25:30,275 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/run_STAR.ok 2026-03-03 19:25:30,277 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam -o /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --remove_dups 2026-03-03 19:25:30,821 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam -o /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --remove_dups 2026-03-03 19:25:30,822 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/mark_dup_reads.ok 2026-03-03 19:25:30,824 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam 2026-03-03 19:25:30,886 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam 2026-03-03 19:25:30,886 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/mark_dups_reads.index.ok 2026-03-03 19:25:30,888 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-03-03 19:25:33,737 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-03-03 19:25:33,737 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 2026-03-03 19:25:33,739 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-03-03 19:25:43,545 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-03-03 19:25:43,546 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 2026-03-03 19:25:43,547 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary 2026-03-03 19:25:43,567 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary 2026-03-03 19:25:43,567 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/coalesce_junc_n_span.ok 2026-03-03 19:25:43,569 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj 2026-03-03 19:25:43,594 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj 2026-03-03 19:25:43,594 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/init_EM_adj_counts.ok 2026-03-03 19:25:43,596 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-03-03 19:25:43,618 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-03-03 19:25:43,618 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/filter_by_frag_threshs.ok 2026-03-03 19:25:43,619 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-03-03 19:25:43,635 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-03-03 19:25:43,635 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_extract_junc_reads.ok 2026-03-03 19:25:43,636 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa - | samtools sort -@ 8 - -o /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam" 2026-03-03 19:25:43,680 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa - | samtools sort -@ 8 - -o /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam" 2026-03-03 19:25:43,680 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_junc_reads_bam.ok 2026-03-03 19:25:43,682 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam 2026-03-03 19:25:43,688 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam 2026-03-03 19:25:43,688 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/samtools_idx_junc_reads_bam.ok 2026-03-03 19:25:43,689 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed 2026-03-03 19:25:43,719 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.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed 2026-03-03 19:25:43,719 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.junction_reads.bam.bam_to_bed.ok 2026-03-03 19:25:43,721 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,722 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,723 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.junction_reads.bam.bedsort.ok 2026-03-03 19:25:43,724 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,730 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,730 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.junction_reads.bam.bgzip.ok 2026-03-03 19:25:43,732 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz 2026-03-03 19:25:43,737 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz 2026-03-03 19:25:43,737 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.junction_reads.bam.tabix.ok 2026-03-03 19:25:43,738 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-03-03 19:25:43,754 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-03-03 19:25:43,754 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/span_reads_acc.ok 2026-03-03 19:25:43,756 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools view -H /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam 2026-03-03 19:25:43,762 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam 2026-03-03 19:25:43,762 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/init_spanning_reads_bam.ok 2026-03-03 19:25:43,763 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa - | samtools sort -@ 8 - -o /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam || : 2026-03-03 19:25:43,803 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa - | samtools sort -@ 8 - -o /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam || : 2026-03-03 19:25:43,803 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_spanning_reads.ok 2026-03-03 19:25:43,804 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam 2026-03-03 19:25:43,809 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam 2026-03-03 19:25:43,809 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/samtools_index_span_reads_bam.ok 2026-03-03 19:25:43,811 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed 2026-03-03 19:25:43,828 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.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed 2026-03-03 19:25:43,828 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bam_to_bed.ok 2026-03-03 19:25:43,830 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,831 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,831 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bedsort.ok 2026-03-03 19:25:43,833 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,838 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 19:25:43,838 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bgzip.ok 2026-03-03 19:25:43,840 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz 2026-03-03 19:25:43,845 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz 2026-03-03 19:25:43,845 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/rna_s1221_S42.spanning_reads.bam.tabix.ok 2026-03-03 19:25:43,847 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam 2026-03-03 19:25:43,850 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam 2026-03-03 19:25:43,850 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/cp_consol_bam.ok 2026-03-03 19:25:43,851 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam 2026-03-03 19:25:43,912 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam 2026-03-03 19:25:43,912 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/index_consol_bam.ok 2026-03-03 19:25:43,914 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 2026-03-03 19:25:45,254 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 2026-03-03 19:25:45,254 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_sam_frag_coordss.ok 2026-03-03 19:25:45,256 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.FusionJuncSpan 2026-03-03 19:25:45,298 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.FusionJuncSpan 2026-03-03 19:25:45,298 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_juncspan_fmt.ok 2026-03-03 19:25:45,300 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.Pfam.gff3 2026-03-03 19:25:45,474 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.LVxD8jMVWP/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.Pfam.gff3 2026-03-03 19:25:45,474 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_pfam_gff3.ok 2026-03-03 19:25:45,476 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.Pfam.bed 2026-03-03 19:25:45,552 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.LVxD8jMVWP/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.Pfam.bed 2026-03-03 19:25:45,552 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_pfam_bed.ok 2026-03-03 19:25:45,554 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.LVxD8jMVWP/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.seqsimilar.gff3 2026-03-03 19:25:45,597 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.LVxD8jMVWP/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.seqsimilar.gff3 2026-03-03 19:25:45,597 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_seqsim_gff3.ok 2026-03-03 19:25:45,599 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.seqsimilar.bed 2026-03-03 19:25:45,624 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.LVxD8jMVWP/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.igv.seqsimilar.bed 2026-03-03 19:25:45,624 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/prep_igv_seqsim_bed.ok 2026-03-03 19:25:45,626 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-03-03 19:25:45,675 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fa > /tmp/nxf.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-03-03 19:25:45,675 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/add_splice_info.ok 2026-03-03 19:25:45,677 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LVxD8jMVWP/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-03-03 19:25:45,866 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.LVxD8jMVWP/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LVxD8jMVWP/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-03-03 19:25:45,866 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/blast_filter.ok 2026-03-03 19:25:45,868 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.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir 2026-03-03 19:25:45,892 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.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir 2026-03-03 19:25:45,892 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/annot_filter.ok 2026-03-03 19:25:45,893 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-03-03 19:25:45,911 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.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-03-03 19:25:45,911 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/EM_adj_counts.ok 2026-03-03 19:25:45,913 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-03-03 19:26:00,097 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-03-03 19:26:00,097 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/add_FFPM.ok 2026-03-03 19:26:00,099 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.LVxD8jMVWP/rna_s1221_S42.fa --gtf /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf > /tmp/nxf.LVxD8jMVWP/fi_workdir/microH.dat 2026-03-03 19:26:00,264 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.LVxD8jMVWP/rna_s1221_S42.fa --gtf /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.gtf > /tmp/nxf.LVxD8jMVWP/fi_workdir/microH.dat 2026-03-03 19:26:00,265 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/microH.dat.ok 2026-03-03 19:26:00,266 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.LVxD8jMVWP/fi_workdir/microH.dat /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-03-03 19:26:00,290 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.LVxD8jMVWP/fi_workdir/microH.dat /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-03-03 19:26:00,290 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/append_microH_info.ok 2026-03-03 19:26:00,292 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.tsv 2026-03-03 19:26:00,294 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.tsv 2026-03-03 19:26:00,294 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/cp_final.ok 2026-03-03 19:26:00,295 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv 2026-03-03 19:26:00,311 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv 2026-03-03 19:26:00,311 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/final.abridged.ok 2026-03-03 19:26:00,313 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.LVxD8jMVWP --json_outfile /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42 2026-03-03 19:26:00,336 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.LVxD8jMVWP --json_outfile /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42 2026-03-03 19:26:00,336 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/create_fi_igvjs.ok 2026-03-03 19:26:00,338 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.LVxD8jMVWP/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fusion_inspector_web.html 2026-03-03 19:26:00,944 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.fusion_inspector_web.html 2026-03-03 19:26:00,945 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/fusion_reports_html.ok 2026-03-03 19:26:00,946 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 2026-03-03 19:26:00,979 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 2026-03-03 19:26:00,979 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/fusion_annotator.ok 2026-03-03 19:26:00,981 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.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-03-03 19:26:01,144 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.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.LVxD8jMVWP/ctat_genome_lib_build_dir > /tmp/nxf.LVxD8jMVWP/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-03-03 19:26:01,144 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.LVxD8jMVWP/chckpts_dir/fusion_coding_region_effect.ok