2026-06-08 09:50:19,250 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_00088_23H5VFLT4_s02.fusionreport.tsv --gtf /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02 --shrink_introns --max_intron_length 1000
2026-06-08 09:50:26,312 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 tih_rna_sample_00088_23H5VFLT4_s02.fusionreport.tsv --gtf /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02 --shrink_introns --max_intron_length 1000
2026-06-08 09:50:26,313 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/fusion_contigs.ok
2026-06-08 09:50:26,315 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fa
2026-06-08 09:50:26,317 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fa
2026-06-08 09:50:26,317 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/cp_contigs_file_workdir
2026-06-08 09:50:26,319 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf
2026-06-08 09:50:26,322 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf
2026-06-08 09:50:26,322 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 09:50:26,323 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf > /tmp/nxf.8mLHDOwlDD/cytoBand.txt
2026-06-08 09:50:26,359 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf > /tmp/nxf.8mLHDOwlDD/cytoBand.txt
2026-06-08 09:50:26,359 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/cytoband.ok
2026-06-08 09:50:26,361 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed
2026-06-08 09:50:26,442 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed
2026-06-08 09:50:26,442 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 09:50:26,444 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed.sorted.bed
2026-06-08 09:50:26,445 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed.sorted.bed
2026-06-08 09:50:26,446 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.bed.bedsort.ok
2026-06-08 09:50:26,447 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed.sorted.bed
2026-06-08 09:50:26,453 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed.sorted.bed
2026-06-08 09:50:26,453 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.bed.bgzip.ok
2026-06-08 09:50:26,455 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed.sorted.bed.gz
2026-06-08 09:50:26,460 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.bed.sorted.bed.gz
2026-06-08 09:50:26,460 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.bed.tabix.ok
2026-06-08 09:50:26,462 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa
2026-06-08 09:50:26,468 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa
2026-06-08 09:50:26,468 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/merged_contig_fai.ok
2026-06-08 09:50:26,470 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fa --max_mate_dist 100000 -G /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf --CPU 8 --out_prefix tih_rna_sample_00088_23H5VFLT4_s02.star --out_dir /tmp/nxf.8mLHDOwlDD/fi_workdir --reads "/tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02_1.fastp.fastq.gz /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02_2.fastp.fastq.gz"
2026-06-08 11:19:20,741 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 88.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fa --max_mate_dist 100000 -G /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf --CPU 8 --out_prefix tih_rna_sample_00088_23H5VFLT4_s02.star --out_dir /tmp/nxf.8mLHDOwlDD/fi_workdir --reads "/tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02_1.fastp.fastq.gz /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02_2.fastp.fastq.gz"
2026-06-08 11:19:20,742 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/run_STAR.ok
2026-06-08 11:19:20,744 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.sortedByCoord.out.bam -o /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:19:26,384 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.sortedByCoord.out.bam -o /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:19:26,384 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/mark_dup_reads.ok
2026-06-08 11:19:26,387 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam
2026-06-08 11:19:27,076 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam
2026-06-08 11:19:27,076 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 11:19:27,078 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:20:01,666 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.58 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:20:01,667 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 11:20:01,669 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:21:57,380 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:21:57,380 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 11:21:57,382 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary
2026-06-08 11:21:57,416 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary
2026-06-08 11:21:57,416 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 11:21:57,417 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:21:57,439 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:21:57,439 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 11:21:57,440 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:21:57,460 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:21:57,461 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 11:21:57,462 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:21:57,476 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:21:57,476 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 11:21:57,478 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa - | samtools sort -@ 8 - -o /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam"
2026-06-08 11:21:57,542 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa - | samtools sort -@ 8 - -o /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam"
2026-06-08 11:21:57,542 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 11:21:57,543 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam
2026-06-08 11:21:57,550 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam
2026-06-08 11:21:57,551 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 11:21:57,552 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed
2026-06-08 11:21:57,617 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed
2026-06-08 11:21:57,617 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bam_to_bed.ok
2026-06-08 11:21:57,619 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,622 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,622 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bedsort.ok
2026-06-08 11:21:57,624 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,632 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,632 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bgzip.ok
2026-06-08 11:21:57,633 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:21:57,639 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:21:57,639 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.junction_reads.bam.tabix.ok
2026-06-08 11:21:57,641 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:21:57,655 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:21:57,655 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/span_reads_acc.ok
2026-06-08 11:21:57,657 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam
2026-06-08 11:21:57,663 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam
2026-06-08 11:21:57,663 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 11:21:57,665 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa - | samtools sort -@ 8 - -o /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam || :
2026-06-08 11:21:57,701 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa - | samtools sort -@ 8 - -o /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam || :
2026-06-08 11:21:57,701 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_spanning_reads.ok
2026-06-08 11:21:57,703 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam
2026-06-08 11:21:57,708 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam
2026-06-08 11:21:57,708 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 11:21:57,710 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed
2026-06-08 11:21:57,725 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed
2026-06-08 11:21:57,725 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bam_to_bed.ok
2026-06-08 11:21:57,726 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,728 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,729 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bedsort.ok
2026-06-08 11:21:57,730 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,735 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:21:57,735 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bgzip.ok
2026-06-08 11:21:57,737 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:21:57,742 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:21:57,742 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/tih_rna_sample_00088_23H5VFLT4_s02.spanning_reads.bam.tabix.ok
2026-06-08 11:21:57,744 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam
2026-06-08 11:21:57,756 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.star.cSorted.dupsMarked.bam /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam
2026-06-08 11:21:57,756 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/cp_consol_bam.ok
2026-06-08 11:21:57,758 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam
2026-06-08 11:21:58,445 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam
2026-06-08 11:21:58,445 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/index_consol_bam.ok
2026-06-08 11:21:58,447 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam --max_insert_size 10000000
2026-06-08 11:22:15,101 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam --max_insert_size 10000000
2026-06-08 11:22:15,101 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 11:22:15,104 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam.frag_coords > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.FusionJuncSpan
2026-06-08 11:22:15,382 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.consolidated.bam.frag_coords > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.FusionJuncSpan
2026-06-08 11:22:15,382 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 11:22:15,384 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.Pfam.gff3
2026-06-08 11:22:15,449 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.Pfam.gff3
2026-06-08 11:22:15,449 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 11:22:15,451 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.Pfam.gff3 > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.Pfam.bed
2026-06-08 11:22:15,492 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.Pfam.gff3 > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.Pfam.bed
2026-06-08 11:22:15,492 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 11:22:15,494 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.seqsimilar.gff3
2026-06-08 11:22:15,520 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.seqsimilar.gff3
2026-06-08 11:22:15,520 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 11:22:15,522 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.seqsimilar.gff3 > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.seqsimilar.bed
2026-06-08 11:22:15,543 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.seqsimilar.gff3 > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.igv.seqsimilar.bed
2026-06-08 11:22:15,543 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 11:22:15,545 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:22:15,578 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa > /tmp/nxf.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:22:15,578 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/add_splice_info.ok
2026-06-08 11:22:15,580 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:22:15,730 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.8mLHDOwlDD/fi_workdir/tih_rna_sample_00088_23H5VFLT4_s02.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:22:15,730 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/blast_filter.ok
2026-06-08 11:22:15,732 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir
2026-06-08 11:22:15,751 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir
2026-06-08 11:22:15,751 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/annot_filter.ok
2026-06-08 11:22:15,753 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:22:15,773 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:22:15,773 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/EM_adj_counts.ok
2026-06-08 11:22:15,775 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02_1.fastp.fastq.gz /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 11:27:57,907 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02_1.fastp.fastq.gz /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 11:27:57,907 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/add_FFPM.ok
2026-06-08 11:27:57,909 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa --gtf /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf > /tmp/nxf.8mLHDOwlDD/fi_workdir/microH.dat
2026-06-08 11:27:57,996 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fa --gtf /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.gtf > /tmp/nxf.8mLHDOwlDD/fi_workdir/microH.dat
2026-06-08 11:27:57,997 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/microH.dat.ok
2026-06-08 11:27:57,999 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.8mLHDOwlDD/fi_workdir/microH.dat /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 11:27:58,030 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.8mLHDOwlDD/fi_workdir/microH.dat /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 11:27:58,030 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/append_microH_info.ok
2026-06-08 11:27:58,032 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.tsv
2026-06-08 11:27:58,035 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.tsv
2026-06-08 11:27:58,035 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/cp_final.ok
2026-06-08 11:27:58,037 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv
2026-06-08 11:27:58,051 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv
2026-06-08 11:27:58,051 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/final.abridged.ok
2026-06-08 11:27:58,053 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.8mLHDOwlDD --json_outfile /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fusion_inspector_web.json --file_prefix tih_rna_sample_00088_23H5VFLT4_s02
2026-06-08 11:27:58,073 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.8mLHDOwlDD --json_outfile /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fusion_inspector_web.json --file_prefix tih_rna_sample_00088_23H5VFLT4_s02
2026-06-08 11:27:58,073 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/create_fi_igvjs.ok
2026-06-08 11:27:58,074 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00088_23H5VFLT4_s02 --html_output /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fusion_inspector_web.html
2026-06-08 11:27:58,476 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00088_23H5VFLT4_s02 --html_output /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.fusion_inspector_web.html
2026-06-08 11:27:58,476 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/fusion_reports_html.ok
2026-06-08 11:27:58,478 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 11:27:58,502 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 11:27:58,502 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/fusion_annotator.ok
2026-06-08 11:27:58,504 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 11:27:58,551 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.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.8mLHDOwlDD/ctat_genome_lib_build_dir > /tmp/nxf.8mLHDOwlDD/tih_rna_sample_00088_23H5VFLT4_s02.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 11:27:58,551 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.8mLHDOwlDD/chckpts_dir/fusion_coding_region_effect.ok