FusionInspector.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (A673_FFPE_RNA_0001_B23LG7FLT4_3)

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/e007397c5e651dca3b1cbee6499b3e/FusionInspector.log
Size: 43.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (A673_FFPE_RNA_0001_B23LG7FLT4_3)
Attempt
Content

2026-05-28 22:35:41,607 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv --gtf /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000 

2026-05-28 22:35:49,133 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv --gtf /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000 

2026-05-28 22:35:49,133 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_contigs.ok

2026-05-28 22:35:49,135 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa

2026-05-28 22:35:49,138 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa

2026-05-28 22:35:49,138 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_contigs_file_workdir

2026-05-28 22:35:49,140 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf

2026-05-28 22:35:49,144 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf

2026-05-28 22:35:49,144 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_gtf_file_workdir.ok

2026-05-28 22:35:49,146 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/cytoBand.txt

2026-05-28 22:35:49,289 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/cytoBand.txt

2026-05-28 22:35:49,289 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cytoband.ok

2026-05-28 22:35:49,291 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed

2026-05-28 22:35:49,484 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed

2026-05-28 22:35:49,484 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-05-28 22:35:49,486 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed

2026-05-28 22:35:49,488 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed

2026-05-28 22:35:49,489 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bedsort.ok

2026-05-28 22:35:49,490 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed

2026-05-28 22:35:49,499 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed

2026-05-28 22:35:49,499 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bgzip.ok

2026-05-28 22:35:49,500 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz

2026-05-28 22:35:49,507 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz

2026-05-28 22:35:49,507 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.tabix.ok

2026-05-28 22:35:49,508 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa

2026-05-28 22:35:49,522 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa

2026-05-28 22:35:49,523 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/merged_contig_fai.ok

2026-05-28 22:35:49,524 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.KXy1ipFxeT/fi_workdir --reads "/tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"

2026-05-28 23:43:45,122 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 67.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.KXy1ipFxeT/fi_workdir --reads "/tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz"

2026-05-28 23:43:45,122 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/run_STAR.ok

2026-05-28 23:43:45,124 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam   -o /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam   --remove_dups 

2026-05-28 23:44:05,617 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam   -o /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam   --remove_dups 

2026-05-28 23:44:05,617 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/mark_dup_reads.ok

2026-05-28 23:44:05,619 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam

2026-05-28 23:44:08,525 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam

2026-05-28 23:44:08,525 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/mark_dups_reads.index.ok

2026-05-28 23:44:08,527 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-05-28 23:46:16,282 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 2.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-05-28 23:46:16,282 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-05-28 23:46:16,284 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-05-28 23:51:51,833 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-05-28 23:51:51,833 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-05-28 23:51:51,836 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary

2026-05-28 23:51:51,993 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary

2026-05-28 23:51:51,994 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/coalesce_junc_n_span.ok

2026-05-28 23:51:51,996 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj

2026-05-28 23:51:52,597 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj

2026-05-28 23:51:52,597 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/init_EM_adj_counts.ok

2026-05-28 23:51:52,600 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-05-28 23:51:52,627 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-05-28 23:51:52,627 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/filter_by_frag_threshs.ok

2026-05-28 23:51:52,629 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-05-28 23:51:52,650 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-05-28 23:51:52,650 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-05-28 23:51:52,652 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam"

2026-05-28 23:51:52,913 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam"

2026-05-28 23:51:52,913 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-05-28 23:51:52,915 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam

2026-05-28 23:51:52,945 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam

2026-05-28 23:51:52,945 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-05-28 23:51:52,947 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed

2026-05-28 23:51:53,656 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed

2026-05-28 23:51:53,656 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bam_to_bed.ok

2026-05-28 23:51:53,658 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,675 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,675 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bedsort.ok

2026-05-28 23:51:53,677 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,719 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,719 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bgzip.ok

2026-05-28 23:51:53,721 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz

2026-05-28 23:51:53,735 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz

2026-05-28 23:51:53,735 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.tabix.ok

2026-05-28 23:51:53,737 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-05-28 23:51:53,757 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-05-28 23:51:53,757 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/span_reads_acc.ok

2026-05-28 23:51:53,759 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam

2026-05-28 23:51:53,765 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam

2026-05-28 23:51:53,765 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/init_spanning_reads_bam.ok

2026-05-28 23:51:53,767 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam || : 

2026-05-28 23:51:53,805 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam || : 

2026-05-28 23:51:53,805 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_spanning_reads.ok

2026-05-28 23:51:53,807 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam

2026-05-28 23:51:53,812 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam

2026-05-28 23:51:53,812 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/samtools_index_span_reads_bam.ok

2026-05-28 23:51:53,814 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed

2026-05-28 23:51:53,831 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed

2026-05-28 23:51:53,831 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bam_to_bed.ok

2026-05-28 23:51:53,833 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,834 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,834 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bedsort.ok

2026-05-28 23:51:53,836 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,841 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed

2026-05-28 23:51:53,841 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bgzip.ok

2026-05-28 23:51:53,843 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz

2026-05-28 23:51:53,848 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz

2026-05-28 23:51:53,848 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.tabix.ok

2026-05-28 23:51:53,850 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam

2026-05-28 23:51:53,886 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam

2026-05-28 23:51:53,886 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_consol_bam.ok

2026-05-28 23:51:53,888 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam

2026-05-28 23:51:56,200 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam

2026-05-28 23:51:56,200 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/index_consol_bam.ok

2026-05-28 23:51:56,202 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000 

2026-05-28 23:52:52,238 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000 

2026-05-28 23:52:52,239 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-05-28 23:52:52,241 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan

2026-05-28 23:52:53,281 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan

2026-05-28 23:52:53,281 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-05-28 23:52:53,283 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 

2026-05-28 23:52:53,399 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 

2026-05-28 23:52:53,399 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_pfam_gff3.ok

2026-05-28 23:52:53,401 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed

2026-05-28 23:52:53,459 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed

2026-05-28 23:52:53,459 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_pfam_bed.ok

2026-05-28 23:52:53,461 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 

2026-05-28 23:52:53,506 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 

2026-05-28 23:52:53,506 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-05-28 23:52:53,508 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed

2026-05-28 23:52:53,536 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed

2026-05-28 23:52:53,536 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_seqsim_bed.ok

2026-05-28 23:52:53,538 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-05-28 23:52:53,674 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-05-28 23:52:53,674 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/add_splice_info.ok

2026-05-28 23:52:53,677 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-05-28 23:52:53,834 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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-05-28 23:52:53,835 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/blast_filter.ok

2026-05-28 23:52:53,837 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir

2026-05-28 23:52:53,859 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir

2026-05-28 23:52:53,859 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/annot_filter.ok

2026-05-28 23:52:53,861 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-05-28 23:52:53,901 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-05-28 23:52:53,901 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/EM_adj_counts.ok

2026-05-28 23:52:53,903 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-05-28 23:58:40,402 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.77 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-05-28 23:58:40,402 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/add_FFPM.ok

2026-05-28 23:58:40,404 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf  > /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat

2026-05-28 23:58:42,684 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf  > /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat

2026-05-28 23:58:42,684 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/microH.dat.ok

2026-05-28 23:58:42,686 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-05-28 23:58:43,163 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-05-28 23:58:43,163 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/append_microH_info.ok

2026-05-28 23:58:43,166 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv

2026-05-28 23:58:43,168 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv

2026-05-28 23:58:43,169 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_final.ok

2026-05-28 23:58:43,170 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv

2026-05-28 23:58:43,185 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv

2026-05-28 23:58:43,185 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/final.abridged.ok

2026-05-28 23:58:43,187 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.KXy1ipFxeT --json_outfile /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3

2026-05-28 23:58:43,208 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.KXy1ipFxeT --json_outfile /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3

2026-05-28 23:58:43,208 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/create_fi_igvjs.ok

2026-05-28 23:58:43,210 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html

2026-05-28 23:58:45,591 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html

2026-05-28 23:58:45,591 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_reports_html.ok

2026-05-28 23:58:45,594 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated 

2026-05-28 23:58:45,620 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated 

2026-05-28 23:58:45,620 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_annotator.ok

2026-05-28 23:58:45,622 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-05-28 23:58:45,687 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-05-28 23:58:45,687 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_coding_region_effect.ok