2026-06-08 10:07:27,646 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_00457_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000
2026-06-08 10:07:34,917 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_00457_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000
2026-06-08 10:07:34,917 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/fusion_contigs.ok
2026-06-08 10:07:34,918 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fa
2026-06-08 10:07:34,921 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fa
2026-06-08 10:07:34,921 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/cp_contigs_file_workdir
2026-06-08 10:07:34,923 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf
2026-06-08 10:07:34,925 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf
2026-06-08 10:07:34,925 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 10:07:34,927 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf > /tmp/nxf.XczuaQ8A6Z/cytoBand.txt
2026-06-08 10:07:34,966 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf > /tmp/nxf.XczuaQ8A6Z/cytoBand.txt
2026-06-08 10:07:34,966 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/cytoband.ok
2026-06-08 10:07:34,968 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed
2026-06-08 10:07:35,052 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed
2026-06-08 10:07:35,052 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 10:07:35,055 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed.sorted.bed
2026-06-08 10:07:35,058 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed.sorted.bed
2026-06-08 10:07:35,058 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.bed.bedsort.ok
2026-06-08 10:07:35,059 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed.sorted.bed
2026-06-08 10:07:35,067 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed.sorted.bed
2026-06-08 10:07:35,067 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.bed.bgzip.ok
2026-06-08 10:07:35,068 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed.sorted.bed.gz
2026-06-08 10:07:35,074 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.bed.sorted.bed.gz
2026-06-08 10:07:35,075 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.bed.tabix.ok
2026-06-08 10:07:35,077 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa
2026-06-08 10:07:35,083 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa
2026-06-08 10:07:35,083 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/merged_contig_fai.ok
2026-06-08 10:07:35,085 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00457_B23WHTKLT4_2.star --out_dir /tmp/nxf.XczuaQ8A6Z/fi_workdir --reads "/tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2_2.fastp.fastq.gz"
2026-06-08 11:14:25,031 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 66.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00457_B23WHTKLT4_2.star --out_dir /tmp/nxf.XczuaQ8A6Z/fi_workdir --reads "/tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2_2.fastp.fastq.gz"
2026-06-08 11:14:25,032 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/run_STAR.ok
2026-06-08 11:14:25,035 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:14:29,573 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:14:29,573 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/mark_dup_reads.ok
2026-06-08 11:14:29,575 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
2026-06-08 11:14:30,102 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
2026-06-08 11:14:30,103 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 11:14:30,105 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:14:56,639 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:14:56,639 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 11:14:56,642 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:15:59,362 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 11:15:59,362 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 11:15:59,364 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary
2026-06-08 11:15:59,407 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary
2026-06-08 11:15:59,407 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 11:15:59,409 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:15:59,664 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
2026-06-08 11:15:59,664 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 11:15:59,666 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:15:59,686 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 11:15:59,686 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 11:15:59,687 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:15:59,701 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 11:15:59,702 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 11:15:59,703 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam"
2026-06-08 11:15:59,874 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam"
2026-06-08 11:15:59,874 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 11:15:59,876 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam
2026-06-08 11:15:59,894 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam
2026-06-08 11:15:59,894 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 11:15:59,896 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed
2026-06-08 11:16:00,313 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed
2026-06-08 11:16:00,313 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok
2026-06-08 11:16:00,315 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,326 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,326 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bedsort.ok
2026-06-08 11:16:00,327 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,352 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,352 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bgzip.ok
2026-06-08 11:16:00,354 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:16:00,363 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 11:16:00,363 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.junction_reads.bam.tabix.ok
2026-06-08 11:16:00,365 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:16:00,379 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 11:16:00,379 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/span_reads_acc.ok
2026-06-08 11:16:00,381 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam
2026-06-08 11:16:00,386 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam
2026-06-08 11:16:00,386 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 11:16:00,388 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam || :
2026-06-08 11:16:00,424 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam || :
2026-06-08 11:16:00,424 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_spanning_reads.ok
2026-06-08 11:16:00,426 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam
2026-06-08 11:16:00,430 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam
2026-06-08 11:16:00,430 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 11:16:00,432 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed
2026-06-08 11:16:00,448 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed
2026-06-08 11:16:00,448 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok
2026-06-08 11:16:00,449 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,451 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,451 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok
2026-06-08 11:16:00,453 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,458 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
2026-06-08 11:16:00,458 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok
2026-06-08 11:16:00,459 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:16:00,464 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 11:16:00,464 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/tih_rna_sample_00457_B23WHTKLT4_2.spanning_reads.bam.tabix.ok
2026-06-08 11:16:00,466 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam
2026-06-08 11:16:00,475 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam
2026-06-08 11:16:00,475 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/cp_consol_bam.ok
2026-06-08 11:16:00,477 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam
2026-06-08 11:16:01,000 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam
2026-06-08 11:16:01,000 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/index_consol_bam.ok
2026-06-08 11:16:01,002 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000
2026-06-08 11:16:13,604 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000
2026-06-08 11:16:13,604 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 11:16:13,606 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.FusionJuncSpan
2026-06-08 11:16:13,846 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.FusionJuncSpan
2026-06-08 11:16:13,846 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 11:16:13,848 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.Pfam.gff3
2026-06-08 11:16:13,903 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.Pfam.gff3
2026-06-08 11:16:13,903 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 11:16:13,905 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.Pfam.bed
2026-06-08 11:16:13,943 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.Pfam.bed
2026-06-08 11:16:13,944 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 11:16:13,945 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.seqsimilar.gff3
2026-06-08 11:16:13,972 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.seqsimilar.gff3
2026-06-08 11:16:13,972 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 11:16:13,974 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.seqsimilar.bed
2026-06-08 11:16:13,994 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.igv.seqsimilar.bed
2026-06-08 11:16:13,994 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 11:16:13,996 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:16:14,032 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa > /tmp/nxf.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 11:16:14,032 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/add_splice_info.ok
2026-06-08 11:16:14,034 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:16:14,179 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.XczuaQ8A6Z/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 11:16:14,179 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/blast_filter.ok
2026-06-08 11:16:14,181 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir
2026-06-08 11:16:14,199 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir
2026-06-08 11:16:14,199 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/annot_filter.ok
2026-06-08 11:16:14,201 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:16:14,300 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 11:16:14,300 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/EM_adj_counts.ok
2026-06-08 11:16:14,302 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 11:22:09,008 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 11:22:09,008 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/add_FFPM.ok
2026-06-08 11:22:09,010 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa --gtf /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf > /tmp/nxf.XczuaQ8A6Z/fi_workdir/microH.dat
2026-06-08 11:22:09,131 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fa --gtf /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.gtf > /tmp/nxf.XczuaQ8A6Z/fi_workdir/microH.dat
2026-06-08 11:22:09,131 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/microH.dat.ok
2026-06-08 11:22:09,132 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.XczuaQ8A6Z/fi_workdir/microH.dat /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 11:22:09,162 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.XczuaQ8A6Z/fi_workdir/microH.dat /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 11:22:09,162 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/append_microH_info.ok
2026-06-08 11:22:09,163 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.tsv
2026-06-08 11:22:09,166 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.tsv
2026-06-08 11:22:09,166 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/cp_final.ok
2026-06-08 11:22:09,167 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
2026-06-08 11:22:09,180 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
2026-06-08 11:22:09,181 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/final.abridged.ok
2026-06-08 11:22:09,182 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.XczuaQ8A6Z --json_outfile /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00457_B23WHTKLT4_2
2026-06-08 11:22:09,202 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.XczuaQ8A6Z --json_outfile /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00457_B23WHTKLT4_2
2026-06-08 11:22:09,202 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/create_fi_igvjs.ok
2026-06-08 11:22:09,204 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00457_B23WHTKLT4_2 --html_output /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fusion_inspector_web.html
2026-06-08 11:22:09,745 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00457_B23WHTKLT4_2 --html_output /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.fusion_inspector_web.html
2026-06-08 11:22:09,745 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/fusion_reports_html.ok
2026-06-08 11:22:09,747 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 11:22:09,772 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 11:22:09,772 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/fusion_annotator.ok
2026-06-08 11:22:09,774 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 11:22:09,812 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.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.XczuaQ8A6Z/ctat_genome_lib_build_dir > /tmp/nxf.XczuaQ8A6Z/tih_rna_sample_00457_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 11:22:09,813 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.XczuaQ8A6Z/chckpts_dir/fusion_coding_region_effect.ok