FusionInspector.log - Workflow Tracker

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-s3-gitlab-results/rnafusion/build2778182/regression-run/62972821/fusioninspector/FusionInspector.log
Size: 39.4 KB
Workflow Run: gitlab-rnafusion-build2778182-regression-run-62972821
Published: Jun 02, 2026 8:06 AM
Content

2026-06-02 14:56:54,368 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1200_S21.fusionreport.tsv --gtf /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21 --shrink_introns --max_intron_length 1000 

2026-06-02 14:57:03,282 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1200_S21.fusionreport.tsv --gtf /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21 --shrink_introns --max_intron_length 1000 

2026-06-02 14:57:03,282 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/fusion_contigs.ok

2026-06-02 14:57:03,283 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fa

2026-06-02 14:57:03,286 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fa

2026-06-02 14:57:03,286 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/cp_contigs_file_workdir

2026-06-02 14:57:03,288 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf

2026-06-02 14:57:03,290 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf

2026-06-02 14:57:03,290 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-02 14:57:03,291 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf > /tmp/nxf.HuzgSmcRUZ/cytoBand.txt

2026-06-02 14:57:03,325 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.HuzgSmcRUZ/rna_s1200_S21.fa /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf > /tmp/nxf.HuzgSmcRUZ/cytoBand.txt

2026-06-02 14:57:03,326 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/cytoband.ok

2026-06-02 14:57:03,327 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed

2026-06-02 14:57:03,426 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.HuzgSmcRUZ/rna_s1200_S21.gtf > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed

2026-06-02 14:57:03,426 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-02 14:57:03,427 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed.sorted.bed

2026-06-02 14:57:03,429 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed.sorted.bed

2026-06-02 14:57:03,429 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.bed.bedsort.ok

2026-06-02 14:57:03,431 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed.sorted.bed

2026-06-02 14:57:03,437 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed.sorted.bed

2026-06-02 14:57:03,437 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.bed.bgzip.ok

2026-06-02 14:57:03,439 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed.sorted.bed.gz

2026-06-02 14:57:03,444 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.bed.sorted.bed.gz

2026-06-02 14:57:03,444 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.bed.tabix.ok

2026-06-02 14:57:03,446 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa

2026-06-02 14:57:03,452 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa

2026-06-02 14:57:03,452 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/merged_contig_fai.ok

2026-06-02 14:57:03,454 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fa --max_mate_dist 100000 -G /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf --CPU 8 --out_prefix rna_s1200_S21.star --out_dir /tmp/nxf.HuzgSmcRUZ/fi_workdir --reads "/tmp/nxf.HuzgSmcRUZ/rna_s1200_S21_1.fastp.fastq.gz /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21_2.fastp.fastq.gz"

2026-06-02 15:06:39,507 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 9.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fa --max_mate_dist 100000 -G /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf --CPU 8 --out_prefix rna_s1200_S21.star --out_dir /tmp/nxf.HuzgSmcRUZ/fi_workdir --reads "/tmp/nxf.HuzgSmcRUZ/rna_s1200_S21_1.fastp.fastq.gz /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21_2.fastp.fastq.gz"

2026-06-02 15:06:39,507 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/run_STAR.ok

2026-06-02 15:06:39,511 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.sortedByCoord.out.bam   -o /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-02 15:06:39,995 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.sortedByCoord.out.bam   -o /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-02 15:06:39,995 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/mark_dup_reads.ok

2026-06-02 15:06:40,000 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam

2026-06-02 15:06:40,061 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam

2026-06-02 15:06:40,062 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/mark_dups_reads.index.ok

2026-06-02 15:06:40,065 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-02 15:06:42,828 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-02 15:06:42,828 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-02 15:06:42,831 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-02 15:06:52,072 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-02 15:06:52,073 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-02 15:06:52,077 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary

2026-06-02 15:06:52,105 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary

2026-06-02 15:06:52,106 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/coalesce_junc_n_span.ok

2026-06-02 15:06:52,109 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj

2026-06-02 15:06:52,134 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj

2026-06-02 15:06:52,134 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/init_EM_adj_counts.ok

2026-06-02 15:06:52,137 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-02 15:06:52,167 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-02 15:06:52,167 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/filter_by_frag_threshs.ok

2026-06-02 15:06:52,170 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-02 15:06:52,192 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-02 15:06:52,192 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-02 15:06:52,195 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam"

2026-06-02 15:06:52,249 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam"

2026-06-02 15:06:52,249 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-02 15:06:52,252 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam

2026-06-02 15:06:52,262 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam

2026-06-02 15:06:52,263 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-02 15:06:52,266 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed

2026-06-02 15:06:52,295 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.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed

2026-06-02 15:06:52,296 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.junction_reads.bam.bam_to_bed.ok

2026-06-02 15:06:52,299 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,302 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,302 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.junction_reads.bam.bedsort.ok

2026-06-02 15:06:52,304 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,313 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,313 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.junction_reads.bam.bgzip.ok

2026-06-02 15:06:52,316 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed.sorted.bed.gz

2026-06-02 15:06:52,324 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.junction_reads.bam.bed.sorted.bed.gz

2026-06-02 15:06:52,324 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.junction_reads.bam.tabix.ok

2026-06-02 15:06:52,327 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-02 15:06:52,344 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-02 15:06:52,345 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/span_reads_acc.ok

2026-06-02 15:06:52,347 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam

2026-06-02 15:06:52,355 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam

2026-06-02 15:06:52,356 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/init_spanning_reads_bam.ok

2026-06-02 15:06:52,358 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam || : 

2026-06-02 15:06:52,400 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam || : 

2026-06-02 15:06:52,400 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_spanning_reads.ok

2026-06-02 15:06:52,403 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam

2026-06-02 15:06:52,410 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam

2026-06-02 15:06:52,410 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-02 15:06:52,412 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed

2026-06-02 15:06:52,431 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.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed

2026-06-02 15:06:52,431 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.spanning_reads.bam.bam_to_bed.ok

2026-06-02 15:06:52,433 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,436 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,436 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.spanning_reads.bam.bedsort.ok

2026-06-02 15:06:52,438 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,444 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed.sorted.bed

2026-06-02 15:06:52,444 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.spanning_reads.bam.bgzip.ok

2026-06-02 15:06:52,446 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed.sorted.bed.gz

2026-06-02 15:06:52,452 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.spanning_reads.bam.bed.sorted.bed.gz

2026-06-02 15:06:52,452 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/rna_s1200_S21.spanning_reads.bam.tabix.ok

2026-06-02 15:06:52,454 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam

2026-06-02 15:06:52,457 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.star.cSorted.dupsMarked.bam /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam

2026-06-02 15:06:52,458 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/cp_consol_bam.ok

2026-06-02 15:06:52,460 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam

2026-06-02 15:06:52,506 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam

2026-06-02 15:06:52,506 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/index_consol_bam.ok

2026-06-02 15:06:52,509 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam --max_insert_size 10000000 

2026-06-02 15:06:53,499 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam --max_insert_size 10000000 

2026-06-02 15:06:53,499 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-02 15:06:53,503 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam.frag_coords > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.FusionJuncSpan

2026-06-02 15:06:53,547 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.consolidated.bam.frag_coords > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.FusionJuncSpan

2026-06-02 15:06:53,547 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-02 15:06:53,550 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.Pfam.gff3 

2026-06-02 15:06:53,655 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.HuzgSmcRUZ/rna_s1200_S21.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.Pfam.gff3 

2026-06-02 15:06:53,655 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-02 15:06:53,657 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.Pfam.gff3 > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.Pfam.bed

2026-06-02 15:06:53,731 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.HuzgSmcRUZ/rna_s1200_S21.igv.Pfam.gff3 > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.Pfam.bed

2026-06-02 15:06:53,731 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-02 15:06:53,734 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.HuzgSmcRUZ/rna_s1200_S21.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.seqsimilar.gff3 

2026-06-02 15:06:53,771 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.HuzgSmcRUZ/rna_s1200_S21.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.seqsimilar.gff3 

2026-06-02 15:06:53,771 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-02 15:06:53,774 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.seqsimilar.gff3 > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.seqsimilar.bed

2026-06-02 15:06:53,817 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.HuzgSmcRUZ/rna_s1200_S21.igv.seqsimilar.gff3 > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.igv.seqsimilar.bed

2026-06-02 15:06:53,818 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-02 15:06:53,820 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-02 15:06:53,854 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fa > /tmp/nxf.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-02 15:06:53,855 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/add_splice_info.ok

2026-06-02 15:06:53,858 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-02 15:06:54,088 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.HuzgSmcRUZ/fi_workdir/rna_s1200_S21.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-02 15:06:54,088 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/blast_filter.ok

2026-06-02 15:06:54,091 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.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir

2026-06-02 15:06:54,121 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.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir

2026-06-02 15:06:54,121 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/annot_filter.ok

2026-06-02 15:06:54,124 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-02 15:06:54,145 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.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-02 15:06:54,145 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/EM_adj_counts.ok

2026-06-02 15:06:54,147 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21_1.fastp.fastq.gz /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-02 15:07:12,968 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.31 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21_1.fastp.fastq.gz /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-02 15:07:12,968 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/add_FFPM.ok

2026-06-02 15:07:12,972 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.HuzgSmcRUZ/rna_s1200_S21.fa --gtf /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/microH.dat

2026-06-02 15:07:13,091 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.HuzgSmcRUZ/rna_s1200_S21.fa --gtf /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.gtf  > /tmp/nxf.HuzgSmcRUZ/fi_workdir/microH.dat

2026-06-02 15:07:13,092 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/microH.dat.ok

2026-06-02 15:07:13,095 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.HuzgSmcRUZ/fi_workdir/microH.dat /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-02 15:07:13,125 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.HuzgSmcRUZ/fi_workdir/microH.dat /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-02 15:07:13,125 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/append_microH_info.ok

2026-06-02 15:07:13,128 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.tsv

2026-06-02 15:07:13,131 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.tsv

2026-06-02 15:07:13,132 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/cp_final.ok

2026-06-02 15:07:13,134 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv

2026-06-02 15:07:13,158 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv

2026-06-02 15:07:13,158 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/final.abridged.ok

2026-06-02 15:07:13,161 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.HuzgSmcRUZ --json_outfile /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fusion_inspector_web.json --file_prefix rna_s1200_S21

2026-06-02 15:07:13,192 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.HuzgSmcRUZ --json_outfile /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fusion_inspector_web.json --file_prefix rna_s1200_S21

2026-06-02 15:07:13,193 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/create_fi_igvjs.ok

2026-06-02 15:07:13,195 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.HuzgSmcRUZ/rna_s1200_S21.fusion_inspector_web.json --input_file_prefix rna_s1200_S21 --html_output /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fusion_inspector_web.html

2026-06-02 15:07:13,596 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.HuzgSmcRUZ/rna_s1200_S21.fusion_inspector_web.json --input_file_prefix rna_s1200_S21 --html_output /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.fusion_inspector_web.html

2026-06-02 15:07:13,597 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/fusion_reports_html.ok

2026-06-02 15:07:13,600 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-02 15:07:13,641 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-02 15:07:13,641 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/fusion_annotator.ok

2026-06-02 15:07:13,643 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.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-02 15:07:13,742 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.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.HuzgSmcRUZ/ctat_genome_lib_build_dir > /tmp/nxf.HuzgSmcRUZ/rna_s1200_S21.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-02 15:07:13,742 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.HuzgSmcRUZ/chckpts_dir/fusion_coding_region_effect.ok