2026-06-08 10:15:51,187 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_00596_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:15:59,207 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00596_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000
2026-06-08 10:15:59,207 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_contigs.ok
2026-06-08 10:15:59,209 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa
2026-06-08 10:15:59,213 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa
2026-06-08 10:15:59,213 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_contigs_file_workdir
2026-06-08 10:15:59,215 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf
2026-06-08 10:15:59,221 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf
2026-06-08 10:15:59,221 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_gtf_file_workdir.ok
2026-06-08 10:15:59,223 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/cytoBand.txt
2026-06-08 10:15:59,363 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/cytoBand.txt
2026-06-08 10:15:59,363 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cytoband.ok
2026-06-08 10:15:59,365 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed
2026-06-08 10:15:59,767 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed
2026-06-08 10:15:59,768 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/merged_contig_gtf_to_bed.ok
2026-06-08 10:15:59,770 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:15:59,772 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:15:59,773 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.bed.bedsort.ok
2026-06-08 10:15:59,774 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:15:59,787 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed
2026-06-08 10:15:59,787 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.bed.bgzip.ok
2026-06-08 10:15:59,789 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed.gz
2026-06-08 10:15:59,796 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed.gz
2026-06-08 10:15:59,797 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.bed.tabix.ok
2026-06-08 10:15:59,798 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools faidx /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa
2026-06-08 10:15:59,811 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa
2026-06-08 10:15:59,811 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/merged_contig_fai.ok
2026-06-08 10:15:59,813 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00596_B23MVV7LT4_1.star --out_dir /tmp/nxf.y4PgUajcQJ/fi_workdir --reads "/tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_2.fastp.fastq.gz"
2026-06-08 11:49:23,386 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 93.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00596_B23MVV7LT4_1.star --out_dir /tmp/nxf.y4PgUajcQJ/fi_workdir --reads "/tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_2.fastp.fastq.gz"
2026-06-08 11:49:23,386 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/run_STAR.ok
2026-06-08 11:49:23,388 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:50:04,416 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups
2026-06-08 11:50:04,417 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/mark_dup_reads.ok
2026-06-08 11:50:04,419 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:50:09,723 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
2026-06-08 11:50:09,723 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/mark_dups_reads.index.ok
2026-06-08 11:50:09,725 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:54:49,419 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 4.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
2026-06-08 11:54:49,419 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
2026-06-08 11:54:49,421 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 12:06:10,727 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 11.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
2026-06-08 12:06:10,727 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
2026-06-08 12:06:10,729 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary
2026-06-08 12:06:10,849 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary
2026-06-08 12:06:10,849 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/coalesce_junc_n_span.ok
2026-06-08 12:06:10,851 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 12:06:10,944 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
2026-06-08 12:06:10,944 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/init_EM_adj_counts.ok
2026-06-08 12:06:10,946 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 12:06:10,972 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
2026-06-08 12:06:10,973 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/filter_by_frag_threshs.ok
2026-06-08 12:06:10,974 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 12:06:10,993 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
2026-06-08 12:06:10,993 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_extract_junc_reads.ok
2026-06-08 12:06:10,995 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam"
2026-06-08 12:06:11,173 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam"
2026-06-08 12:06:11,173 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_junc_reads_bam.ok
2026-06-08 12:06:11,176 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam
2026-06-08 12:06:11,193 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam
2026-06-08 12:06:11,194 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/samtools_idx_junc_reads_bam.ok
2026-06-08 12:06:11,195 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed
2026-06-08 12:06:11,523 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed
2026-06-08 12:06:11,524 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
2026-06-08 12:06:11,526 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,535 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,535 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
2026-06-08 12:06:11,536 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,562 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,562 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
2026-06-08 12:06:11,564 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 12:06:11,574 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
2026-06-08 12:06:11,575 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.tabix.ok
2026-06-08 12:06:11,576 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 12:06:11,594 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
2026-06-08 12:06:11,595 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/span_reads_acc.ok
2026-06-08 12:06:11,597 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools view -H /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 12:06:11,603 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 12:06:11,603 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/init_spanning_reads_bam.ok
2026-06-08 12:06:11,605 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam || :
2026-06-08 12:06:11,644 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam || :
2026-06-08 12:06:11,644 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_spanning_reads.ok
2026-06-08 12:06:11,646 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 12:06:11,652 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam
2026-06-08 12:06:11,652 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/samtools_index_span_reads_bam.ok
2026-06-08 12:06:11,654 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed
2026-06-08 12:06:11,673 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed
2026-06-08 12:06:11,673 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
2026-06-08 12:06:11,675 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,677 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,677 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
2026-06-08 12:06:11,679 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,685 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
2026-06-08 12:06:11,685 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
2026-06-08 12:06:11,687 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 12:06:11,692 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
2026-06-08 12:06:11,692 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
2026-06-08 12:06:11,694 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam
2026-06-08 12:06:11,758 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam
2026-06-08 12:06:11,759 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_consol_bam.ok
2026-06-08 12:06:11,760 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam
2026-06-08 12:06:15,981 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.07 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam
2026-06-08 12:06:15,982 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/index_consol_bam.ok
2026-06-08 12:06:15,984 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 12:08:01,058 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 1.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000
2026-06-08 12:08:01,058 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_sam_frag_coordss.ok
2026-06-08 12:08:01,060 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.FusionJuncSpan
2026-06-08 12:08:02,862 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.FusionJuncSpan
2026-06-08 12:08:02,863 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_juncspan_fmt.ok
2026-06-08 12:08:02,867 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.gff3
2026-06-08 12:08:03,110 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.gff3
2026-06-08 12:08:03,110 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_pfam_gff3.ok
2026-06-08 12:08:03,112 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.bed
2026-06-08 12:08:03,226 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.bed
2026-06-08 12:08:03,226 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_pfam_bed.ok
2026-06-08 12:08:03,228 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.gff3
2026-06-08 12:08:03,294 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.gff3
2026-06-08 12:08:03,294 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_seqsim_gff3.ok
2026-06-08 12:08:03,296 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.bed
2026-06-08 12:08:03,318 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.bed
2026-06-08 12:08:03,318 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_seqsim_bed.ok
2026-06-08 12:08:03,320 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 12:08:03,428 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
2026-06-08 12:08:03,429 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/add_splice_info.ok
2026-06-08 12:08:03,430 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 12:08:03,601 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
2026-06-08 12:08:03,601 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/blast_filter.ok
2026-06-08 12:08:03,603 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir
2026-06-08 12:08:03,628 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir
2026-06-08 12:08:03,628 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/annot_filter.ok
2026-06-08 12:08:03,630 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 12:08:03,677 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
2026-06-08 12:08:03,677 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/EM_adj_counts.ok
2026-06-08 12:08:03,679 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:13:52,483 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 5.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
2026-06-08 12:13:52,484 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/add_FFPM.ok
2026-06-08 12:13:52,486 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa --gtf /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/fi_workdir/microH.dat
2026-06-08 12:13:52,941 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa --gtf /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/fi_workdir/microH.dat
2026-06-08 12:13:52,941 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/microH.dat.ok
2026-06-08 12:13:52,943 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.y4PgUajcQJ/fi_workdir/microH.dat /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:13:53,046 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.y4PgUajcQJ/fi_workdir/microH.dat /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
2026-06-08 12:13:53,047 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/append_microH_info.ok
2026-06-08 12:13:53,049 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv
2026-06-08 12:13:53,052 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv
2026-06-08 12:13:53,052 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_final.ok
2026-06-08 12:13:53,054 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:13:53,073 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
2026-06-08 12:13:53,073 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/final.abridged.ok
2026-06-08 12:13:53,075 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.y4PgUajcQJ --json_outfile /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00596_B23MVV7LT4_1
2026-06-08 12:13:53,097 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.y4PgUajcQJ --json_outfile /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00596_B23MVV7LT4_1
2026-06-08 12:13:53,097 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/create_fi_igvjs.ok
2026-06-08 12:13:53,099 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00596_B23MVV7LT4_1 --html_output /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.html
2026-06-08 12:13:54,945 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.03 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00596_B23MVV7LT4_1 --html_output /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.html
2026-06-08 12:13:54,945 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_reports_html.ok
2026-06-08 12:13:54,947 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:13:54,986 INFO Pipeliner.Pipeliner.run at 136 :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated
2026-06-08 12:13:54,986 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_annotator.ok
2026-06-08 12:13:54,988 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:13:55,172 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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
2026-06-08 12:13:55,173 INFO Pipeliner.Pipeliner.run_cmd at 21 :
Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_coding_region_effect.ok