2026-06-08 10:36:41,045 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 2026-06-08 10:36:47,955 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 2026-06-08 10:36:47,955 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/fusion_contigs.ok 2026-06-08 10:36:47,957 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:36:47,960 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:36:47,960 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/cp_contigs_file_workdir 2026-06-08 10:36:47,961 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf 2026-06-08 10:36:47,963 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf 2026-06-08 10:36:47,963 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/cp_gtf_file_workdir.ok 2026-06-08 10:36:47,965 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.g00bJqrkzU/cytoBand.txt 2026-06-08 10:36:47,992 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.g00bJqrkzU/cytoBand.txt 2026-06-08 10:36:47,992 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/cytoband.ok 2026-06-08 10:36:47,994 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed 2026-06-08 10:36:48,054 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed 2026-06-08 10:36:48,054 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/merged_contig_gtf_to_bed.ok 2026-06-08 10:36:48,055 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:36:48,057 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:36:48,058 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok 2026-06-08 10:36:48,059 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:36:48,067 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed 2026-06-08 10:36:48,067 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok 2026-06-08 10:36:48,068 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz 2026-06-08 10:36:48,073 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz 2026-06-08 10:36:48,074 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok 2026-06-08 10:36:48,075 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools faidx /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:36:48,081 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa 2026-06-08 10:36:48,081 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/merged_contig_fai.ok 2026-06-08 10:36:48,082 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.g00bJqrkzU/fi_workdir --reads "/tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" 2026-06-08 11:16:12,844 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 39.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.g00bJqrkzU/fi_workdir --reads "/tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" 2026-06-08 11:16:12,844 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/run_STAR.ok 2026-06-08 11:16:12,846 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 11:16:18,564 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 11:16:18,564 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/mark_dup_reads.ok 2026-06-08 11:16:18,566 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam 2026-06-08 11:16:19,327 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam 2026-06-08 11:16:19,327 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/mark_dups_reads.index.ok 2026-06-08 11:16:19,329 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 11:17:02,868 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 11:17:02,869 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 2026-06-08 11:17:02,871 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 11:18:29,670 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 1.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 11:18:29,671 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 2026-06-08 11:18:29,673 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary 2026-06-08 11:18:29,697 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary 2026-06-08 11:18:29,698 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/coalesce_junc_n_span.ok 2026-06-08 11:18:29,699 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-08 11:18:29,721 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj 2026-06-08 11:18:29,721 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/init_EM_adj_counts.ok 2026-06-08 11:18:29,723 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 11:18:29,742 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 11:18:29,742 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/filter_by_frag_threshs.ok 2026-06-08 11:18:29,743 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 11:18:29,757 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 11:18:29,757 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_extract_junc_reads.ok 2026-06-08 11:18:29,759 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" 2026-06-08 11:18:29,834 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" 2026-06-08 11:18:29,834 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_junc_reads_bam.ok 2026-06-08 11:18:29,836 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam 2026-06-08 11:18:29,843 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam 2026-06-08 11:18:29,843 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/samtools_idx_junc_reads_bam.ok 2026-06-08 11:18:29,845 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed 2026-06-08 11:18:29,946 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed 2026-06-08 11:18:29,946 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok 2026-06-08 11:18:29,948 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:18:29,952 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:18:29,952 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok 2026-06-08 11:18:29,954 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:18:29,962 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed 2026-06-08 11:18:29,962 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok 2026-06-08 11:18:29,964 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 11:18:29,970 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 11:18:29,970 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok 2026-06-08 11:18:29,972 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 11:18:29,985 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 11:18:29,985 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/span_reads_acc.ok 2026-06-08 11:18:29,987 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools view -H /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:18:29,992 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:18:29,992 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/init_spanning_reads_bam.ok 2026-06-08 11:18:29,994 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 2026-06-08 11:18:30,010 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 2026-06-08 11:18:30,010 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_spanning_reads.ok 2026-06-08 11:18:30,011 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:18:30,016 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam 2026-06-08 11:18:30,016 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/samtools_index_span_reads_bam.ok 2026-06-08 11:18:30,017 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed 2026-06-08 11:18:30,032 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed 2026-06-08 11:18:30,033 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok 2026-06-08 11:18:30,034 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:18:30,036 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:18:30,036 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok 2026-06-08 11:18:30,038 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:18:30,042 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:18:30,043 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok 2026-06-08 11:18:30,044 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 11:18:30,049 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 11:18:30,049 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok 2026-06-08 11:18:30,051 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:18:30,063 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:18:30,063 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/cp_consol_bam.ok 2026-06-08 11:18:30,065 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:18:30,802 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam 2026-06-08 11:18:30,802 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/index_consol_bam.ok 2026-06-08 11:18:30,805 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 2026-06-08 11:18:52,481 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 2026-06-08 11:18:52,481 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_sam_frag_coordss.ok 2026-06-08 11:18:52,483 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan 2026-06-08 11:18:52,937 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan 2026-06-08 11:18:52,937 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_juncspan_fmt.ok 2026-06-08 11:18:52,939 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 2026-06-08 11:18:52,977 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 2026-06-08 11:18:52,977 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_pfam_gff3.ok 2026-06-08 11:18:52,979 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed 2026-06-08 11:18:53,005 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed 2026-06-08 11:18:53,006 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_pfam_bed.ok 2026-06-08 11:18:53,007 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 2026-06-08 11:18:53,031 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 2026-06-08 11:18:53,032 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_seqsim_gff3.ok 2026-06-08 11:18:53,033 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed 2026-06-08 11:18:53,054 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed 2026-06-08 11:18:53,054 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/prep_igv_seqsim_bed.ok 2026-06-08 11:18:53,056 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 11:18:53,083 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 11:18:53,083 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/add_splice_info.ok 2026-06-08 11:18:53,084 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-08 11:18:53,230 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.g00bJqrkzU/fi_workdir/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-08 11:18:53,231 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/blast_filter.ok 2026-06-08 11:18:53,233 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir 2026-06-08 11:18:53,251 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir 2026-06-08 11:18:53,251 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/annot_filter.ok 2026-06-08 11:18:53,253 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 11:18:53,274 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 11:18:53,274 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/EM_adj_counts.ok 2026-06-08 11:18:53,276 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 11:23:12,799 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 4.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 11:23:12,799 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/add_FFPM.ok 2026-06-08 11:23:12,802 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.g00bJqrkzU/fi_workdir/microH.dat 2026-06-08 11:23:12,861 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.g00bJqrkzU/fi_workdir/microH.dat 2026-06-08 11:23:12,861 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/microH.dat.ok 2026-06-08 11:23:12,863 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.g00bJqrkzU/fi_workdir/microH.dat /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 11:23:12,886 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.g00bJqrkzU/fi_workdir/microH.dat /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 11:23:12,886 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/append_microH_info.ok 2026-06-08 11:23:12,888 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv 2026-06-08 11:23:12,890 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv 2026-06-08 11:23:12,890 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/cp_final.ok 2026-06-08 11:23:12,892 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv 2026-06-08 11:23:12,905 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv 2026-06-08 11:23:12,906 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/final.abridged.ok 2026-06-08 11:23:12,907 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.g00bJqrkzU --json_outfile /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 2026-06-08 11:23:12,928 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.g00bJqrkzU --json_outfile /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 2026-06-08 11:23:12,928 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/create_fi_igvjs.ok 2026-06-08 11:23:12,929 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html 2026-06-08 11:23:13,237 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html 2026-06-08 11:23:13,237 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/fusion_reports_html.ok 2026-06-08 11:23:13,239 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 11:23:13,263 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 11:23:13,264 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/fusion_annotator.ok 2026-06-08 11:23:13,265 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 11:23:13,302 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.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.g00bJqrkzU/ctat_genome_lib_build_dir > /tmp/nxf.g00bJqrkzU/1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 11:23:13,302 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.g00bJqrkzU/chckpts_dir/fusion_coding_region_effect.ok