2026-06-08 10:19:47,984 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 2026-06-08 10:19:54,945 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_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 2026-06-08 10:19:54,946 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/fusion_contigs.ok 2026-06-08 10:19:54,947 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa 2026-06-08 10:19:54,950 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa 2026-06-08 10:19:54,950 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/cp_contigs_file_workdir 2026-06-08 10:19:54,951 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf 2026-06-08 10:19:54,953 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf 2026-06-08 10:19:54,953 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/cp_gtf_file_workdir.ok 2026-06-08 10:19:54,955 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Cm4IsnbmGj/cytoBand.txt 2026-06-08 10:19:55,012 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Cm4IsnbmGj/cytoBand.txt 2026-06-08 10:19:55,013 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/cytoband.ok 2026-06-08 10:19:55,014 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed 2026-06-08 10:19:55,054 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed 2026-06-08 10:19:55,054 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/merged_contig_gtf_to_bed.ok 2026-06-08 10:19:55,055 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed 2026-06-08 10:19:55,057 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed 2026-06-08 10:19:55,057 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok 2026-06-08 10:19:55,059 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed 2026-06-08 10:19:55,070 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed 2026-06-08 10:19:55,070 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok 2026-06-08 10:19:55,072 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz 2026-06-08 10:19:55,077 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz 2026-06-08 10:19:55,077 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok 2026-06-08 10:19:55,079 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools faidx /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa 2026-06-08 10:19:55,087 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa 2026-06-08 10:19:55,087 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/merged_contig_fai.ok 2026-06-08 10:19:55,089 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.Cm4IsnbmGj/fi_workdir --reads "/tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" 2026-06-08 11:34:59,822 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 75.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.Cm4IsnbmGj/fi_workdir --reads "/tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" 2026-06-08 11:34:59,822 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/run_STAR.ok 2026-06-08 11:34:59,824 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 11:35:42,900 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.72 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups 2026-06-08 11:35:42,900 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/mark_dup_reads.ok 2026-06-08 11:35:42,902 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam 2026-06-08 11:35:48,009 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam 2026-06-08 11:35:48,009 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/mark_dups_reads.index.ok 2026-06-08 11:35:48,011 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 11:41:37,752 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 5.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-06-08 11:41:37,752 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 2026-06-08 11:41:37,754 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 11:52:25,505 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 10.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-06-08 11:52:25,506 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 2026-06-08 11:52:25,508 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary 2026-06-08 11:52:25,522 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary 2026-06-08 11:52:25,522 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/coalesce_junc_n_span.ok 2026-06-08 11:52:25,524 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj 2026-06-08 11:52:25,538 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj 2026-06-08 11:52:25,538 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/init_EM_adj_counts.ok 2026-06-08 11:52:25,540 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 11:52:25,558 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-06-08 11:52:25,558 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/filter_by_frag_threshs.ok 2026-06-08 11:52:25,559 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 11:52:25,572 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-06-08 11:52:25,572 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_extract_junc_reads.ok 2026-06-08 11:52:25,574 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam" 2026-06-08 11:52:25,613 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam" 2026-06-08 11:52:25,613 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_junc_reads_bam.ok 2026-06-08 11:52:25,615 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam 2026-06-08 11:52:25,620 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam 2026-06-08 11:52:25,621 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/samtools_idx_junc_reads_bam.ok 2026-06-08 11:52:25,623 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed 2026-06-08 11:52:25,642 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed 2026-06-08 11:52:25,642 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok 2026-06-08 11:52:25,644 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,646 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,646 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok 2026-06-08 11:52:25,648 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,653 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,653 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok 2026-06-08 11:52:25,655 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 11:52:25,660 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz 2026-06-08 11:52:25,660 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok 2026-06-08 11:52:25,662 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 11:52:25,674 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-06-08 11:52:25,675 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/span_reads_acc.ok 2026-06-08 11:52:25,676 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools view -H /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam 2026-06-08 11:52:25,682 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam 2026-06-08 11:52:25,682 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/init_spanning_reads_bam.ok 2026-06-08 11:52:25,683 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : 2026-06-08 11:52:25,699 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : 2026-06-08 11:52:25,699 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_spanning_reads.ok 2026-06-08 11:52:25,701 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam 2026-06-08 11:52:25,705 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam 2026-06-08 11:52:25,706 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/samtools_index_span_reads_bam.ok 2026-06-08 11:52:25,707 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed 2026-06-08 11:52:25,722 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed 2026-06-08 11:52:25,722 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok 2026-06-08 11:52:25,724 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,726 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,726 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok 2026-06-08 11:52:25,727 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,732 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed 2026-06-08 11:52:25,732 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok 2026-06-08 11:52:25,734 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 11:52:25,739 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz 2026-06-08 11:52:25,739 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok 2026-06-08 11:52:25,741 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam 2026-06-08 11:52:25,819 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam 2026-06-08 11:52:25,819 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/cp_consol_bam.ok 2026-06-08 11:52:25,821 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam 2026-06-08 11:52:30,927 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam 2026-06-08 11:52:30,928 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/index_consol_bam.ok 2026-06-08 11:52:30,930 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 2026-06-08 11:55:00,599 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 2.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 2026-06-08 11:55:00,599 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_sam_frag_coordss.ok 2026-06-08 11:55:00,601 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan 2026-06-08 11:55:03,247 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan 2026-06-08 11:55:03,247 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_juncspan_fmt.ok 2026-06-08 11:55:03,249 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 2026-06-08 11:55:03,279 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 2026-06-08 11:55:03,279 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_pfam_gff3.ok 2026-06-08 11:55:03,281 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed 2026-06-08 11:55:03,305 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed 2026-06-08 11:55:03,305 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_pfam_bed.ok 2026-06-08 11:55:03,307 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 2026-06-08 11:55:03,329 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 2026-06-08 11:55:03,329 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_seqsim_gff3.ok 2026-06-08 11:55:03,331 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed 2026-06-08 11:55:03,352 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed 2026-06-08 11:55:03,352 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/prep_igv_seqsim_bed.ok 2026-06-08 11:55:03,354 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 11:55:03,410 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-06-08 11:55:03,410 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/add_splice_info.ok 2026-06-08 11:55:03,412 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-08 11:55:03,558 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.Cm4IsnbmGj/fi_workdir/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-06-08 11:55:03,558 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/blast_filter.ok 2026-06-08 11:55:03,560 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir 2026-06-08 11:55:03,578 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir 2026-06-08 11:55:03,579 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/annot_filter.ok 2026-06-08 11:55:03,580 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 11:55:03,594 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-06-08 11:55:03,594 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/EM_adj_counts.ok 2026-06-08 11:55:03,596 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 12:00:15,841 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 5.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-06-08 12:00:15,841 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/add_FFPM.ok 2026-06-08 12:00:15,843 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Cm4IsnbmGj/fi_workdir/microH.dat 2026-06-08 12:00:16,036 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.Cm4IsnbmGj/fi_workdir/microH.dat 2026-06-08 12:00:16,037 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/microH.dat.ok 2026-06-08 12:00:16,039 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Cm4IsnbmGj/fi_workdir/microH.dat /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 12:00:16,059 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.Cm4IsnbmGj/fi_workdir/microH.dat /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-06-08 12:00:16,059 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/append_microH_info.ok 2026-06-08 12:00:16,061 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv 2026-06-08 12:00:16,063 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv 2026-06-08 12:00:16,063 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/cp_final.ok 2026-06-08 12:00:16,065 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv 2026-06-08 12:00:16,078 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv 2026-06-08 12:00:16,078 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/final.abridged.ok 2026-06-08 12:00:16,080 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.Cm4IsnbmGj --json_outfile /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 2026-06-08 12:00:16,101 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.Cm4IsnbmGj --json_outfile /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 2026-06-08 12:00:16,101 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/create_fi_igvjs.ok 2026-06-08 12:00:16,103 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html 2026-06-08 12:00:16,940 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_FM_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html 2026-06-08 12:00:16,940 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/fusion_reports_html.ok 2026-06-08 12:00:16,942 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 12:00:16,962 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 2026-06-08 12:00:16,962 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/fusion_annotator.ok 2026-06-08 12:00:16,964 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 12:00:16,990 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.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.Cm4IsnbmGj/ctat_genome_lib_build_dir > /tmp/nxf.Cm4IsnbmGj/1173_FM_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-06-08 12:00:16,990 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.Cm4IsnbmGj/chckpts_dir/fusion_coding_region_effect.ok