2026-06-08 10:07:12,236 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_00588_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:07:19,332 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_00588_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:07:19,332 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/fusion_contigs.ok
2026-06-08 10:07:19,334 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fa
2026-06-08 10:07:19,337 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fa
2026-06-08 10:07:19,337 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/cp_contigs_file_workdir
2026-06-08 10:07:19,338 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf
2026-06-08 10:07:19,341 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf
2026-06-08 10:07:19,341 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 10:07:19,342 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf > /tmp/nxf.XJBuVHMciG/cytoBand.txt
2026-06-08 10:07:19,393 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf > /tmp/nxf.XJBuVHMciG/cytoBand.txt
2026-06-08 10:07:19,393 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/cytoband.ok
2026-06-08 10:07:19,395 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed
2026-06-08 10:07:19,522 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed
2026-06-08 10:07:19,523 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 10:07:19,524 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:07:19,527 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:07:19,527 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.bed.bedsort.ok
2026-06-08 10:07:19,528 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:07:19,537 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:07:19,537 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.bed.bgzip.ok
2026-06-08 10:07:19,539 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed.sorted.bed.gz
2026-06-08 10:07:19,544 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.bed.sorted.bed.gz
2026-06-08 10:07:19,545 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.bed.tabix.ok
2026-06-08 10:07:19,546 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa
2026-06-08 10:07:19,553 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa
2026-06-08 10:07:19,553 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/merged_contig_fai.ok
2026-06-08 10:07:19,555 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00588_B23MVV7LT4_1.star --out_dir /tmp/nxf.XJBuVHMciG/fi_workdir --reads "/tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1_2.fastp.fastq.gz"
2026-06-08 11:12:01,105 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 64.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00588_B23MVV7LT4_1.star --out_dir /tmp/nxf.XJBuVHMciG/fi_workdir --reads "/tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1_2.fastp.fastq.gz"
2026-06-08 11:12:01,106 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/run_STAR.ok
2026-06-08 11:12:01,108 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:13:30,687 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:13:30,687 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/mark_dup_reads.ok
2026-06-08 11:13:30,689 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:13:41,007 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.17 minutes. CMD: samtools index /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:13:41,007 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 11:13:41,009 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:23:42,996 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 10.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:23:42,996 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 11:23:42,998 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:54:12,317 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 30.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:54:12,317 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 11:54:12,319 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary
2026-06-08 11:54:12,668 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary
2026-06-08 11:54:12,668 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 11:54:12,670 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:54:12,735 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:54:12,735 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 11:54:12,737 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:54:12,772 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:54:12,772 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 11:54:12,773 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:54:12,801 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:54:12,801 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 11:54:12,802 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam"
2026-06-08 11:54:12,867 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam"
2026-06-08 11:54:12,867 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 11:54:12,869 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam
2026-06-08 11:54:12,876 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam
2026-06-08 11:54:12,876 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 11:54:12,877 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed
2026-06-08 11:54:12,947 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed
2026-06-08 11:54:12,947 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
2026-06-08 11:54:12,948 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:54:12,951 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:54:12,951 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
2026-06-08 11:54:12,953 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:54:12,962 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 11:54:12,962 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
2026-06-08 11:54:12,964 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:54:12,970 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:54:12,970 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.junction_reads.bam.tabix.ok
2026-06-08 11:54:12,971 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:54:12,998 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:54:12,998 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/span_reads_acc.ok
2026-06-08 11:54:13,000 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:54:13,005 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:54:13,005 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 11:54:13,006 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam || :
2026-06-08 11:54:13,042 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam || :
2026-06-08 11:54:13,042 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_spanning_reads.ok
2026-06-08 11:54:13,044 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:54:13,048 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 11:54:13,048 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 11:54:13,050 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed
2026-06-08 11:54:13,065 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed
2026-06-08 11:54:13,065 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
2026-06-08 11:54:13,066 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:54:13,068 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:54:13,068 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
2026-06-08 11:54:13,069 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:54:13,074 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:54:13,074 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
2026-06-08 11:54:13,075 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:54:13,080 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:54:13,080 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/tih_rna_sample_00588_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
2026-06-08 11:54:13,082 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:54:13,211 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:54:13,211 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/cp_consol_bam.ok
2026-06-08 11:54:13,213 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:54:23,492 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.17 minutes. CMD: samtools index /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam
2026-06-08 11:54:23,492 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/index_consol_bam.ok
2026-06-08 11:54:23,494 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 11:59:16,526 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 4.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 11:59:16,526 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 11:59:16,528 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.FusionJuncSpan
2026-06-08 11:59:21,644 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.FusionJuncSpan
2026-06-08 11:59:21,644 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 11:59:21,645 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.Pfam.gff3
2026-06-08 11:59:21,727 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.Pfam.gff3
2026-06-08 11:59:21,727 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 11:59:21,728 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.Pfam.bed
2026-06-08 11:59:21,771 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.Pfam.bed
2026-06-08 11:59:21,771 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 11:59:21,773 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.seqsimilar.gff3
2026-06-08 11:59:21,803 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.seqsimilar.gff3
2026-06-08 11:59:21,804 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 11:59:21,805 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.seqsimilar.bed
2026-06-08 11:59:21,825 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.igv.seqsimilar.bed
2026-06-08 11:59:21,825 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 11:59:21,827 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:59:21,875 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa > /tmp/nxf.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:59:21,875 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/add_splice_info.ok
2026-06-08 11:59:21,876 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:59:22,034 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.XJBuVHMciG/fi_workdir/tih_rna_sample_00588_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:59:22,034 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/blast_filter.ok
2026-06-08 11:59:22,036 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir
2026-06-08 11:59:22,060 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir
2026-06-08 11:59:22,060 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/annot_filter.ok
2026-06-08 11:59:22,062 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:59:22,086 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:59:22,086 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/EM_adj_counts.ok
2026-06-08 11:59:22,087 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:04:57,152 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.58 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:04:57,152 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/add_FFPM.ok
2026-06-08 12:04:57,154 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa --gtf /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf > /tmp/nxf.XJBuVHMciG/fi_workdir/microH.dat
2026-06-08 12:04:57,301 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fa --gtf /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.gtf > /tmp/nxf.XJBuVHMciG/fi_workdir/microH.dat
2026-06-08 12:04:57,301 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/microH.dat.ok
2026-06-08 12:04:57,303 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.XJBuVHMciG/fi_workdir/microH.dat /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:04:57,385 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.XJBuVHMciG/fi_workdir/microH.dat /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:04:57,385 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/append_microH_info.ok
2026-06-08 12:04:57,387 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.tsv
2026-06-08 12:04:57,390 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.tsv
2026-06-08 12:04:57,390 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/cp_final.ok
2026-06-08 12:04:57,392 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:04:57,408 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:04:57,408 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/final.abridged.ok
2026-06-08 12:04:57,410 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.XJBuVHMciG --json_outfile /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00588_B23MVV7LT4_1
2026-06-08 12:04:57,430 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.XJBuVHMciG --json_outfile /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00588_B23MVV7LT4_1
2026-06-08 12:04:57,430 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/create_fi_igvjs.ok
2026-06-08 12:04:57,431 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00588_B23MVV7LT4_1 --html_output /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fusion_inspector_web.html
2026-06-08 12:04:58,022 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00588_B23MVV7LT4_1 --html_output /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.fusion_inspector_web.html
2026-06-08 12:04:58,022 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/fusion_reports_html.ok
2026-06-08 12:04:58,024 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:04:58,049 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:04:58,049 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/fusion_annotator.ok
2026-06-08 12:04:58,050 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:04:58,126 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.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XJBuVHMciG/ctat_genome_lib_build_dir > /tmp/nxf.XJBuVHMciG/tih_rna_sample_00588_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:04:58,126 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XJBuVHMciG/chckpts_dir/fusion_coding_region_effect.ok