2026-06-08 10:35:50,748 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00569_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:35:58,450 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00569_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:35:58,450 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_contigs.ok
2026-06-08 10:35:58,452 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa
2026-06-08 10:35:58,455 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa
2026-06-08 10:35:58,455 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_contigs_file_workdir
2026-06-08 10:35:58,457 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf
2026-06-08 10:35:58,459 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf
2026-06-08 10:35:58,460 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 10:35:58,461 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/cytoBand.txt
2026-06-08 10:35:58,531 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/cytoBand.txt
2026-06-08 10:35:58,531 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cytoband.ok
2026-06-08 10:35:58,533 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed
2026-06-08 10:35:58,665 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed
2026-06-08 10:35:58,666 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 10:35:58,667 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:35:58,670 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:35:58,670 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.bed.bedsort.ok
2026-06-08 10:35:58,671 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:35:58,680 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:35:58,680 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.bed.bgzip.ok
2026-06-08 10:35:58,682 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed.gz
2026-06-08 10:35:58,687 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.bed.sorted.bed.gz
2026-06-08 10:35:58,688 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.bed.tabix.ok
2026-06-08 10:35:58,690 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa
2026-06-08 10:35:58,698 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa
2026-06-08 10:35:58,698 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/merged_contig_fai.ok
2026-06-08 10:35:58,700 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00569_B23MVV7LT4_1.star --out_dir /tmp/nxf.jfar3XoMy6/fi_workdir --reads "/tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_2.fastp.fastq.gz"
2026-06-08 11:39:23,713 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 63.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00569_B23MVV7LT4_1.star --out_dir /tmp/nxf.jfar3XoMy6/fi_workdir --reads "/tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_2.fastp.fastq.gz"
2026-06-08 11:39:23,713 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/run_STAR.ok
2026-06-08 11:39:23,716 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:39:40,868 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:39:40,868 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/mark_dup_reads.ok
2026-06-08 11:39:40,870 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:39:42,940 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:39:42,941 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 11:39:42,943 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:41:38,625 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:41:38,625 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 11:41:38,627 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:46:37,552 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 4.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:46:37,553 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 11:46:37,555 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary
2026-06-08 11:46:37,637 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary
2026-06-08 11:46:37,637 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 11:46:37,639 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:46:37,953 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:46:37,953 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 11:46:37,954 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:46:37,977 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:46:37,977 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 11:46:37,979 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:46:37,996 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:46:37,996 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 11:46:37,998 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam"
2026-06-08 11:46:38,090 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam"
2026-06-08 11:46:38,090 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 11:46:38,092 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam
2026-06-08 11:46:38,102 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam
2026-06-08 11:46:38,102 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 11:46:38,104 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed
2026-06-08 11:46:38,263 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed
2026-06-08 11:46:38,263 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
2026-06-08 11:46:38,265 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,270 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,270 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
2026-06-08 11:46:38,272 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,286 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,286 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
2026-06-08 11:46:38,288 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:46:38,295 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:46:38,295 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.junction_reads.bam.tabix.ok
2026-06-08 11:46:38,297 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:46:38,313 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:46:38,313 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/span_reads_acc.ok
2026-06-08 11:46:38,315 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:46:38,321 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:46:38,321 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 11:46:38,323 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam || :
2026-06-08 11:46:38,359 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam || :
2026-06-08 11:46:38,359 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_spanning_reads.ok
2026-06-08 11:46:38,361 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:46:38,365 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:46:38,366 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 11:46:38,367 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed
2026-06-08 11:46:38,382 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed
2026-06-08 11:46:38,382 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
2026-06-08 11:46:38,384 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,386 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,387 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
2026-06-08 11:46:38,388 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,393 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:46:38,393 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
2026-06-08 11:46:38,395 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:46:38,400 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:46:38,400 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/tih_rna_sample_00569_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
2026-06-08 11:46:38,402 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:46:38,431 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:46:38,431 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_consol_bam.ok
2026-06-08 11:46:38,433 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:46:40,498 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:46:40,499 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/index_consol_bam.ok
2026-06-08 11:46:40,501 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 11:47:34,280 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 11:47:34,280 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 11:47:34,283 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.FusionJuncSpan
2026-06-08 11:47:35,264 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.FusionJuncSpan
2026-06-08 11:47:35,265 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 11:47:35,267 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.gff3
2026-06-08 11:47:35,359 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.gff3
2026-06-08 11:47:35,359 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 11:47:35,361 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.bed
2026-06-08 11:47:35,425 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.Pfam.bed
2026-06-08 11:47:35,425 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 11:47:35,427 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.gff3
2026-06-08 11:47:35,461 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.gff3
2026-06-08 11:47:35,461 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 11:47:35,463 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.bed
2026-06-08 11:47:35,483 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.igv.seqsimilar.bed
2026-06-08 11:47:35,483 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 11:47:35,485 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:47:35,547 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa > /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:47:35,547 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/add_splice_info.ok
2026-06-08 11:47:35,548 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:47:35,697 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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:47:35,698 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/blast_filter.ok
2026-06-08 11:47:35,699 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir
2026-06-08 11:47:35,719 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir
2026-06-08 11:47:35,719 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/annot_filter.ok
2026-06-08 11:47:35,721 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:47:35,872 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:47:35,872 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/EM_adj_counts.ok
2026-06-08 11:47:35,874 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 11:53:12,005 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 11:53:12,005 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/add_FFPM.ok
2026-06-08 11:53:12,007 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa --gtf /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/fi_workdir/microH.dat
2026-06-08 11:53:12,233 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fa --gtf /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf > /tmp/nxf.jfar3XoMy6/fi_workdir/microH.dat
2026-06-08 11:53:12,233 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/microH.dat.ok
2026-06-08 11:53:12,234 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.jfar3XoMy6/fi_workdir/microH.dat /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 11:53:12,273 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.jfar3XoMy6/fi_workdir/microH.dat /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 11:53:12,273 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/append_microH_info.ok
2026-06-08 11:53:12,275 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv
2026-06-08 11:53:12,278 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv
2026-06-08 11:53:12,278 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/cp_final.ok
2026-06-08 11:53:12,280 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 11:53:12,294 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 11:53:12,294 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/final.abridged.ok
2026-06-08 11:53:12,296 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.jfar3XoMy6 --json_outfile /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00569_B23MVV7LT4_1
2026-06-08 11:53:12,316 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.jfar3XoMy6 --json_outfile /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00569_B23MVV7LT4_1
2026-06-08 11:53:12,316 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/create_fi_igvjs.ok
2026-06-08 11:53:12,318 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00569_B23MVV7LT4_1 --html_output /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.html
2026-06-08 11:53:13,207 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00569_B23MVV7LT4_1 --html_output /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.fusion_inspector_web.html
2026-06-08 11:53:13,207 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_reports_html.ok
2026-06-08 11:53:13,209 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 11:53:13,238 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 11:53:13,238 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_annotator.ok
2026-06-08 11:53:13,240 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 11:53:13,305 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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.jfar3XoMy6/ctat_genome_lib_build_dir > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 11:53:13,305 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.jfar3XoMy6/chckpts_dir/fusion_coding_region_effect.ok