FusionInspector.log - Workflow Tracker

File Info

Filename: FusionInspector.log
Full Path: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/sm_testing/small_test_SMR_v3_100b4b86_4/fusioninspector/FusionInspector.log
Size: 39.4 KB
Workflow Run: small_test_SMR_v3_100b4b86_4
Published: Feb 25, 2026 11:06 AM
Content

2026-02-25 18:59:58,005 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.cAnLsCEo04/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.cAnLsCEo04/rna_s1221_S42 --shrink_introns --max_intron_length 1000 

2026-02-25 19:00:07,599 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.16 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.cAnLsCEo04/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.cAnLsCEo04/rna_s1221_S42 --shrink_introns --max_intron_length 1000 

2026-02-25 19:00:07,599 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/fusion_contigs.ok

2026-02-25 19:00:07,601 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fa

2026-02-25 19:00:07,604 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fa

2026-02-25 19:00:07,604 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/cp_contigs_file_workdir

2026-02-25 19:00:07,607 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf

2026-02-25 19:00:07,609 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf

2026-02-25 19:00:07,609 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/cp_gtf_file_workdir.ok

2026-02-25 19:00:07,611 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf > /tmp/nxf.cAnLsCEo04/cytoBand.txt

2026-02-25 19:00:07,630 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.cAnLsCEo04/rna_s1221_S42.fa /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf > /tmp/nxf.cAnLsCEo04/cytoBand.txt

2026-02-25 19:00:07,630 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/cytoband.ok

2026-02-25 19:00:07,632 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed

2026-02-25 19:00:07,677 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.cAnLsCEo04/rna_s1221_S42.gtf > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed

2026-02-25 19:00:07,677 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-02-25 19:00:07,679 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed.sorted.bed

2026-02-25 19:00:07,681 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed.sorted.bed

2026-02-25 19:00:07,681 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.bed.bedsort.ok

2026-02-25 19:00:07,683 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed.sorted.bed

2026-02-25 19:00:07,689 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed.sorted.bed

2026-02-25 19:00:07,689 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.bed.bgzip.ok

2026-02-25 19:00:07,691 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed.sorted.bed.gz

2026-02-25 19:00:07,697 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cAnLsCEo04/rna_s1221_S42.bed.sorted.bed.gz

2026-02-25 19:00:07,697 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.bed.tabix.ok

2026-02-25 19:00:07,699 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa

2026-02-25 19:00:07,705 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa

2026-02-25 19:00:07,705 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/merged_contig_fai.ok

2026-02-25 19:00:07,706 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.cAnLsCEo04/fi_workdir --reads "/tmp/nxf.cAnLsCEo04/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.cAnLsCEo04/rna_s1221_S42_2.fastp.fastq.gz"

2026-02-25 19:06:31,065 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 6.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.cAnLsCEo04/fi_workdir --reads "/tmp/nxf.cAnLsCEo04/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.cAnLsCEo04/rna_s1221_S42_2.fastp.fastq.gz"

2026-02-25 19:06:31,066 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/run_STAR.ok

2026-02-25 19:06:31,068 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam   -o /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam   --remove_dups 

2026-02-25 19:06:31,118 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam   -o /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam   --remove_dups 

2026-02-25 19:06:31,119 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/mark_dup_reads.ok

2026-02-25 19:06:31,121 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam

2026-02-25 19:06:31,128 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam

2026-02-25 19:06:31,128 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/mark_dups_reads.index.ok

2026-02-25 19:06:31,130 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-02-25 19:06:31,181 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-02-25 19:06:31,181 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-02-25 19:06:31,183 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-02-25 19:06:31,234 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-02-25 19:06:31,234 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-02-25 19:06:31,236 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary

2026-02-25 19:06:31,252 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary

2026-02-25 19:06:31,252 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/coalesce_junc_n_span.ok

2026-02-25 19:06:31,255 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj

2026-02-25 19:06:31,272 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj

2026-02-25 19:06:31,272 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/init_EM_adj_counts.ok

2026-02-25 19:06:31,273 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-02-25 19:06:31,295 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-02-25 19:06:31,295 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/filter_by_frag_threshs.ok

2026-02-25 19:06:31,298 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-02-25 19:06:31,313 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-02-25 19:06:31,313 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-02-25 19:06:31,315 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam"

2026-02-25 19:06:31,359 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam"

2026-02-25 19:06:31,359 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-02-25 19:06:31,361 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam

2026-02-25 19:06:31,368 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam

2026-02-25 19:06:31,368 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-02-25 19:06:31,370 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed

2026-02-25 19:06:31,389 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.cAnLsCEo04/rna_s1221_S42.junction_reads.bam > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed

2026-02-25 19:06:31,389 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.junction_reads.bam.bam_to_bed.ok

2026-02-25 19:06:31,391 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,393 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,393 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.junction_reads.bam.bedsort.ok

2026-02-25 19:06:31,395 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,401 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,401 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.junction_reads.bam.bgzip.ok

2026-02-25 19:06:31,402 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz

2026-02-25 19:06:31,408 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cAnLsCEo04/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz

2026-02-25 19:06:31,409 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.junction_reads.bam.tabix.ok

2026-02-25 19:06:31,410 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-02-25 19:06:31,426 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-02-25 19:06:31,426 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/span_reads_acc.ok

2026-02-25 19:06:31,428 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam

2026-02-25 19:06:31,434 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam

2026-02-25 19:06:31,434 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/init_spanning_reads_bam.ok

2026-02-25 19:06:31,436 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam || : 

2026-02-25 19:06:31,457 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam || : 

2026-02-25 19:06:31,457 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_spanning_reads.ok

2026-02-25 19:06:31,459 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam

2026-02-25 19:06:31,465 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam

2026-02-25 19:06:31,465 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/samtools_index_span_reads_bam.ok

2026-02-25 19:06:31,467 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed

2026-02-25 19:06:31,485 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.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed

2026-02-25 19:06:31,485 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bam_to_bed.ok

2026-02-25 19:06:31,487 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,489 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,489 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bedsort.ok

2026-02-25 19:06:31,490 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,496 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-02-25 19:06:31,496 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bgzip.ok

2026-02-25 19:06:31,498 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz

2026-02-25 19:06:31,503 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cAnLsCEo04/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz

2026-02-25 19:06:31,504 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/rna_s1221_S42.spanning_reads.bam.tabix.ok

2026-02-25 19:06:31,505 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam

2026-02-25 19:06:31,507 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam

2026-02-25 19:06:31,507 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/cp_consol_bam.ok

2026-02-25 19:06:31,509 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam

2026-02-25 19:06:31,515 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam

2026-02-25 19:06:31,515 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/index_consol_bam.ok

2026-02-25 19:06:31,517 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 

2026-02-25 19:06:31,551 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 

2026-02-25 19:06:31,551 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-02-25 19:06:31,553 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.FusionJuncSpan

2026-02-25 19:06:31,569 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.cAnLsCEo04/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.FusionJuncSpan

2026-02-25 19:06:31,569 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-02-25 19:06:31,571 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.Pfam.gff3 

2026-02-25 19:06:31,603 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.cAnLsCEo04/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.Pfam.gff3 

2026-02-25 19:06:31,604 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_pfam_gff3.ok

2026-02-25 19:06:31,605 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.Pfam.bed

2026-02-25 19:06:31,633 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.cAnLsCEo04/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.Pfam.bed

2026-02-25 19:06:31,634 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_pfam_bed.ok

2026-02-25 19:06:31,636 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.cAnLsCEo04/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.seqsimilar.gff3 

2026-02-25 19:06:31,662 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.cAnLsCEo04/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.seqsimilar.gff3 

2026-02-25 19:06:31,662 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-02-25 19:06:31,664 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.seqsimilar.bed

2026-02-25 19:06:31,690 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.cAnLsCEo04/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.igv.seqsimilar.bed

2026-02-25 19:06:31,690 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/prep_igv_seqsim_bed.ok

2026-02-25 19:06:31,692 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-02-25 19:06:31,711 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa > /tmp/nxf.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-02-25 19:06:31,712 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/add_splice_info.ok

2026-02-25 19:06:31,713 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.cAnLsCEo04/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-02-25 19:06:31,898 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.cAnLsCEo04/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.cAnLsCEo04/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-02-25 19:06:31,899 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/blast_filter.ok

2026-02-25 19:06:31,900 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.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir

2026-02-25 19:06:31,923 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.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir

2026-02-25 19:06:31,923 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/annot_filter.ok

2026-02-25 19:06:31,924 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-02-25 19:06:31,940 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.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-02-25 19:06:31,940 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/EM_adj_counts.ok

2026-02-25 19:06:31,942 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-02-25 19:06:32,102 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-02-25 19:06:32,102 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/add_FFPM.ok

2026-02-25 19:06:32,104 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.cAnLsCEo04/rna_s1221_S42.fa --gtf /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf  > /tmp/nxf.cAnLsCEo04/fi_workdir/microH.dat

2026-02-25 19:06:32,131 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fa --gtf /tmp/nxf.cAnLsCEo04/rna_s1221_S42.gtf  > /tmp/nxf.cAnLsCEo04/fi_workdir/microH.dat

2026-02-25 19:06:32,131 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/microH.dat.ok

2026-02-25 19:06:32,133 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.cAnLsCEo04/fi_workdir/microH.dat /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-02-25 19:06:32,150 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.cAnLsCEo04/fi_workdir/microH.dat /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-02-25 19:06:32,151 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/append_microH_info.ok

2026-02-25 19:06:32,152 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.tsv

2026-02-25 19:06:32,155 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cAnLsCEo04/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.tsv

2026-02-25 19:06:32,155 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/cp_final.ok

2026-02-25 19:06:32,156 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv

2026-02-25 19:06:32,172 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv

2026-02-25 19:06:32,172 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/final.abridged.ok

2026-02-25 19:06:32,174 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.cAnLsCEo04 --json_outfile /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42

2026-02-25 19:06:32,197 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.cAnLsCEo04 --json_outfile /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42

2026-02-25 19:06:32,197 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/create_fi_igvjs.ok

2026-02-25 19:06:32,199 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.cAnLsCEo04/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fusion_inspector_web.html

2026-02-25 19:06:32,329 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 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.cAnLsCEo04/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.cAnLsCEo04/rna_s1221_S42.fusion_inspector_web.html

2026-02-25 19:06:32,329 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/fusion_reports_html.ok

2026-02-25 19:06:32,331 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 

2026-02-25 19:06:32,355 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 

2026-02-25 19:06:32,355 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/fusion_annotator.ok

2026-02-25 19:06:32,357 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.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-02-25 19:06:32,385 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.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.cAnLsCEo04/ctat_genome_lib_build_dir > /tmp/nxf.cAnLsCEo04/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-02-25 19:06:32,386 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.cAnLsCEo04/chckpts_dir/fusion_coding_region_effect.ok