FusionInspector.log - Workflow Tracker

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-s3-gitlab-results/rnafusion/build2781274/regression-run/63055280/fusioninspector/FusionInspector.log
Size: 39.4 KB
Workflow Run: gitlab-rnafusion-build2781274-regression-run-63055280
Published: Jun 02, 2026 9:21 PM
Content

2026-06-03 04:17:26,272 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ghsShRqOOa/rna_s1221_S42 --shrink_introns --max_intron_length 1000 

2026-06-03 04:17:33,156 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ghsShRqOOa/rna_s1221_S42 --shrink_introns --max_intron_length 1000 

2026-06-03 04:17:33,157 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/fusion_contigs.ok

2026-06-03 04:17:33,158 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fa

2026-06-03 04:17:33,160 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fa

2026-06-03 04:17:33,160 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/cp_contigs_file_workdir

2026-06-03 04:17:33,162 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf

2026-06-03 04:17:33,164 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf

2026-06-03 04:17:33,164 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-03 04:17:33,165 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf > /tmp/nxf.ghsShRqOOa/cytoBand.txt

2026-06-03 04:17:33,200 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.ghsShRqOOa/rna_s1221_S42.fa /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf > /tmp/nxf.ghsShRqOOa/cytoBand.txt

2026-06-03 04:17:33,200 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/cytoband.ok

2026-06-03 04:17:33,201 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed

2026-06-03 04:17:33,299 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.ghsShRqOOa/rna_s1221_S42.gtf > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed

2026-06-03 04:17:33,299 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-03 04:17:33,301 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed.sorted.bed

2026-06-03 04:17:33,303 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed.sorted.bed

2026-06-03 04:17:33,303 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.bed.bedsort.ok

2026-06-03 04:17:33,304 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed.sorted.bed

2026-06-03 04:17:33,310 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed.sorted.bed

2026-06-03 04:17:33,311 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.bed.bgzip.ok

2026-06-03 04:17:33,312 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed.sorted.bed.gz

2026-06-03 04:17:33,317 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ghsShRqOOa/rna_s1221_S42.bed.sorted.bed.gz

2026-06-03 04:17:33,317 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.bed.tabix.ok

2026-06-03 04:17:33,319 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa

2026-06-03 04:17:33,325 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa

2026-06-03 04:17:33,325 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/merged_contig_fai.ok

2026-06-03 04:17:33,327 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.ghsShRqOOa/fi_workdir --reads "/tmp/nxf.ghsShRqOOa/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.ghsShRqOOa/rna_s1221_S42_2.fastp.fastq.gz"

2026-06-03 04:25:20,258 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 7.78 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.ghsShRqOOa/fi_workdir --reads "/tmp/nxf.ghsShRqOOa/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.ghsShRqOOa/rna_s1221_S42_2.fastp.fastq.gz"

2026-06-03 04:25:20,258 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/run_STAR.ok

2026-06-03 04:25:20,260 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam   -o /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-03 04:25:20,626 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam   -o /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-03 04:25:20,626 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/mark_dup_reads.ok

2026-06-03 04:25:20,628 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam

2026-06-03 04:25:20,671 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam

2026-06-03 04:25:20,671 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/mark_dups_reads.index.ok

2026-06-03 04:25:20,673 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-03 04:25:22,341 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-03 04:25:22,342 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-03 04:25:22,343 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-03 04:25:27,748 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-03 04:25:27,748 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-03 04:25:27,749 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary

2026-06-03 04:25:27,764 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary

2026-06-03 04:25:27,764 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/coalesce_junc_n_span.ok

2026-06-03 04:25:27,766 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj

2026-06-03 04:25:27,780 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj

2026-06-03 04:25:27,780 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/init_EM_adj_counts.ok

2026-06-03 04:25:27,782 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-03 04:25:27,799 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-03 04:25:27,799 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/filter_by_frag_threshs.ok

2026-06-03 04:25:27,801 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-03 04:25:27,813 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-03 04:25:27,813 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-03 04:25:27,815 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam"

2026-06-03 04:25:27,854 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam"

2026-06-03 04:25:27,854 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-03 04:25:27,856 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam

2026-06-03 04:25:27,860 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam

2026-06-03 04:25:27,861 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-03 04:25:27,862 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed

2026-06-03 04:25:27,883 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.ghsShRqOOa/rna_s1221_S42.junction_reads.bam > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed

2026-06-03 04:25:27,883 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.junction_reads.bam.bam_to_bed.ok

2026-06-03 04:25:27,884 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,886 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,886 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.junction_reads.bam.bedsort.ok

2026-06-03 04:25:27,888 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,893 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,893 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.junction_reads.bam.bgzip.ok

2026-06-03 04:25:27,895 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz

2026-06-03 04:25:27,900 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ghsShRqOOa/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz

2026-06-03 04:25:27,900 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.junction_reads.bam.tabix.ok

2026-06-03 04:25:27,901 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-03 04:25:27,914 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-03 04:25:27,914 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/span_reads_acc.ok

2026-06-03 04:25:27,916 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam

2026-06-03 04:25:27,921 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam

2026-06-03 04:25:27,921 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/init_spanning_reads_bam.ok

2026-06-03 04:25:27,923 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam || : 

2026-06-03 04:25:27,959 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam || : 

2026-06-03 04:25:27,959 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_spanning_reads.ok

2026-06-03 04:25:27,960 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam

2026-06-03 04:25:27,965 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam

2026-06-03 04:25:27,965 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-03 04:25:27,967 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed

2026-06-03 04:25:27,982 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.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed

2026-06-03 04:25:27,982 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bam_to_bed.ok

2026-06-03 04:25:27,983 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,985 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,985 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bedsort.ok

2026-06-03 04:25:27,986 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,991 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-06-03 04:25:27,991 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bgzip.ok

2026-06-03 04:25:27,992 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz

2026-06-03 04:25:27,997 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ghsShRqOOa/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz

2026-06-03 04:25:27,997 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/rna_s1221_S42.spanning_reads.bam.tabix.ok

2026-06-03 04:25:27,999 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam

2026-06-03 04:25:28,001 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam

2026-06-03 04:25:28,001 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/cp_consol_bam.ok

2026-06-03 04:25:28,002 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam

2026-06-03 04:25:28,045 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam

2026-06-03 04:25:28,045 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/index_consol_bam.ok

2026-06-03 04:25:28,046 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 

2026-06-03 04:25:28,863 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 

2026-06-03 04:25:28,863 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-03 04:25:28,864 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.FusionJuncSpan

2026-06-03 04:25:28,890 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.ghsShRqOOa/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.FusionJuncSpan

2026-06-03 04:25:28,890 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-03 04:25:28,892 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.Pfam.gff3 

2026-06-03 04:25:28,964 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.ghsShRqOOa/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.Pfam.gff3 

2026-06-03 04:25:28,964 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-03 04:25:28,966 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.Pfam.bed

2026-06-03 04:25:29,004 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.ghsShRqOOa/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.Pfam.bed

2026-06-03 04:25:29,005 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-03 04:25:29,006 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.ghsShRqOOa/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.seqsimilar.gff3 

2026-06-03 04:25:29,034 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.ghsShRqOOa/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.seqsimilar.gff3 

2026-06-03 04:25:29,034 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-03 04:25:29,036 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.seqsimilar.bed

2026-06-03 04:25:29,056 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.ghsShRqOOa/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.igv.seqsimilar.bed

2026-06-03 04:25:29,057 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-03 04:25:29,059 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-03 04:25:29,087 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fa > /tmp/nxf.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-03 04:25:29,087 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/add_splice_info.ok

2026-06-03 04:25:29,089 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ghsShRqOOa/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-03 04:25:29,231 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.ghsShRqOOa/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ghsShRqOOa/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-03 04:25:29,231 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/blast_filter.ok

2026-06-03 04:25:29,233 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.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir

2026-06-03 04:25:29,250 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.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir

2026-06-03 04:25:29,250 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/annot_filter.ok

2026-06-03 04:25:29,251 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-03 04:25:29,265 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.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-03 04:25:29,265 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/EM_adj_counts.ok

2026-06-03 04:25:29,267 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-03 04:25:42,034 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-03 04:25:42,034 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/add_FFPM.ok

2026-06-03 04:25:42,036 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.ghsShRqOOa/rna_s1221_S42.fa --gtf /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf  > /tmp/nxf.ghsShRqOOa/fi_workdir/microH.dat

2026-06-03 04:25:42,116 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.ghsShRqOOa/rna_s1221_S42.fa --gtf /tmp/nxf.ghsShRqOOa/rna_s1221_S42.gtf  > /tmp/nxf.ghsShRqOOa/fi_workdir/microH.dat

2026-06-03 04:25:42,116 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/microH.dat.ok

2026-06-03 04:25:42,118 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.ghsShRqOOa/fi_workdir/microH.dat /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-03 04:25:42,137 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.ghsShRqOOa/fi_workdir/microH.dat /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-03 04:25:42,137 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/append_microH_info.ok

2026-06-03 04:25:42,139 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.tsv

2026-06-03 04:25:42,141 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ghsShRqOOa/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.tsv

2026-06-03 04:25:42,141 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/cp_final.ok

2026-06-03 04:25:42,142 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv

2026-06-03 04:25:42,155 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv

2026-06-03 04:25:42,155 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/final.abridged.ok

2026-06-03 04:25:42,157 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.ghsShRqOOa --json_outfile /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42

2026-06-03 04:25:42,178 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.ghsShRqOOa --json_outfile /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42

2026-06-03 04:25:42,178 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/create_fi_igvjs.ok

2026-06-03 04:25:42,179 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.ghsShRqOOa/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fusion_inspector_web.html

2026-06-03 04:25:42,555 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.ghsShRqOOa/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.ghsShRqOOa/rna_s1221_S42.fusion_inspector_web.html

2026-06-03 04:25:42,555 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/fusion_reports_html.ok

2026-06-03 04:25:42,557 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-03 04:25:42,582 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-03 04:25:42,582 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/fusion_annotator.ok

2026-06-03 04:25:42,584 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.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-03 04:25:42,646 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.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.ghsShRqOOa/ctat_genome_lib_build_dir > /tmp/nxf.ghsShRqOOa/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-03 04:25:42,646 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.ghsShRqOOa/chckpts_dir/fusion_coding_region_effect.ok