FusionInspector.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (A673_FFPE_RNA_0001_B23LG7FLT4_2)

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/51db993b97e0852cf8d02b02163edf/FusionInspector.log
Size: 43.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (A673_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt
Content

2026-05-28 23:26:10,410 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_2.fusionreport.tsv --gtf /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --shrink_introns --max_intron_length 1000 

2026-05-28 23:26:17,937 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_2.fusionreport.tsv --gtf /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --shrink_introns --max_intron_length 1000 

2026-05-28 23:26:17,937 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_contigs.ok

2026-05-28 23:26:17,939 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa

2026-05-28 23:26:17,942 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa

2026-05-28 23:26:17,942 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_contigs_file_workdir

2026-05-28 23:26:17,944 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf

2026-05-28 23:26:17,947 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf

2026-05-28 23:26:17,947 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_gtf_file_workdir.ok

2026-05-28 23:26:17,949 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/cytoBand.txt

2026-05-28 23:26:18,096 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/cytoBand.txt

2026-05-28 23:26:18,097 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cytoband.ok

2026-05-28 23:26:18,099 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed

2026-05-28 23:26:18,314 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed

2026-05-28 23:26:18,314 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-05-28 23:26:18,316 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed

2026-05-28 23:26:18,319 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed

2026-05-28 23:26:18,319 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.bedsort.ok

2026-05-28 23:26:18,320 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed

2026-05-28 23:26:18,331 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed

2026-05-28 23:26:18,332 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.bgzip.ok

2026-05-28 23:26:18,333 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed.gz

2026-05-28 23:26:18,340 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.sorted.bed.gz

2026-05-28 23:26:18,340 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.bed.tabix.ok

2026-05-28 23:26:18,342 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa

2026-05-28 23:26:18,356 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa

2026-05-28 23:26:18,356 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/merged_contig_fai.ok

2026-05-28 23:26:18,358 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2.star --out_dir /tmp/nxf.7E4AVD1Zcz/fi_workdir --reads "/tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz"

2026-05-29 00:20:44,263 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 54.43 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2.star --out_dir /tmp/nxf.7E4AVD1Zcz/fi_workdir --reads "/tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz"

2026-05-29 00:20:44,263 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/run_STAR.ok

2026-05-29 00:20:44,265 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 

2026-05-29 00:21:04,749 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 

2026-05-29 00:21:04,749 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/mark_dup_reads.ok

2026-05-29 00:21:04,752 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam

2026-05-29 00:21:07,198 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam

2026-05-29 00:21:07,198 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/mark_dups_reads.index.ok

2026-05-29 00:21:07,200 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-05-29 00:23:16,519 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 2.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-05-29 00:23:16,519 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-05-29 00:23:16,521 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-05-29 00:28:56,948 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-05-29 00:28:56,948 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-05-29 00:28:56,950 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary

2026-05-29 00:28:57,129 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary

2026-05-29 00:28:57,129 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/coalesce_junc_n_span.ok

2026-05-29 00:28:57,131 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj

2026-05-29 00:28:57,835 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj

2026-05-29 00:28:57,836 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/init_EM_adj_counts.ok

2026-05-29 00:28:57,838 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-05-29 00:28:57,866 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-05-29 00:28:57,866 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/filter_by_frag_threshs.ok

2026-05-29 00:28:57,868 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-05-29 00:28:57,890 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-05-29 00:28:57,890 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-05-29 00:28:57,892 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam"

2026-05-29 00:28:58,148 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam"

2026-05-29 00:28:58,148 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-05-29 00:28:58,150 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam

2026-05-29 00:28:58,180 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam

2026-05-29 00:28:58,180 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-05-29 00:28:58,182 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed

2026-05-29 00:28:58,860 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed

2026-05-29 00:28:58,860 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bam_to_bed.ok

2026-05-29 00:28:58,862 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed

2026-05-29 00:28:58,878 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed

2026-05-29 00:28:58,878 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bedsort.ok

2026-05-29 00:28:58,879 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed

2026-05-29 00:28:58,921 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed

2026-05-29 00:28:58,921 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bgzip.ok

2026-05-29 00:28:58,923 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed.gz

2026-05-29 00:28:58,935 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.bed.sorted.bed.gz

2026-05-29 00:28:58,935 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.junction_reads.bam.tabix.ok

2026-05-29 00:28:58,937 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-05-29 00:28:58,958 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-05-29 00:28:58,958 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/span_reads_acc.ok

2026-05-29 00:28:58,959 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam

2026-05-29 00:28:58,964 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam

2026-05-29 00:28:58,964 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/init_spanning_reads_bam.ok

2026-05-29 00:28:58,966 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam || : 

2026-05-29 00:28:59,004 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam || : 

2026-05-29 00:28:59,004 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_spanning_reads.ok

2026-05-29 00:28:59,005 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam

2026-05-29 00:28:59,010 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam

2026-05-29 00:28:59,010 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/samtools_index_span_reads_bam.ok

2026-05-29 00:28:59,012 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed

2026-05-29 00:28:59,029 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed

2026-05-29 00:28:59,029 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bam_to_bed.ok

2026-05-29 00:28:59,030 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed

2026-05-29 00:28:59,032 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed

2026-05-29 00:28:59,032 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bedsort.ok

2026-05-29 00:28:59,034 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed

2026-05-29 00:28:59,038 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed

2026-05-29 00:28:59,038 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bgzip.ok

2026-05-29 00:28:59,040 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed.gz

2026-05-29 00:28:59,045 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.bed.sorted.bed.gz

2026-05-29 00:28:59,045 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_2.spanning_reads.bam.tabix.ok

2026-05-29 00:28:59,047 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam

2026-05-29 00:28:59,085 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam

2026-05-29 00:28:59,085 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_consol_bam.ok

2026-05-29 00:28:59,087 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam

2026-05-29 00:29:01,523 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam

2026-05-29 00:29:01,523 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/index_consol_bam.ok

2026-05-29 00:29:01,525 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam --max_insert_size 10000000 

2026-05-29 00:29:59,391 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam --max_insert_size 10000000 

2026-05-29 00:29:59,391 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-05-29 00:29:59,393 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.FusionJuncSpan

2026-05-29 00:30:00,452 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.FusionJuncSpan

2026-05-29 00:30:00,452 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-05-29 00:30:00,453 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.gff3 

2026-05-29 00:30:00,563 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.gff3 

2026-05-29 00:30:00,563 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_pfam_gff3.ok

2026-05-29 00:30:00,565 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.bed

2026-05-29 00:30:00,620 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.Pfam.bed

2026-05-29 00:30:00,620 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_pfam_bed.ok

2026-05-29 00:30:00,622 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.gff3 

2026-05-29 00:30:00,668 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.gff3 

2026-05-29 00:30:00,668 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-05-29 00:30:00,670 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.bed

2026-05-29 00:30:00,696 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.igv.seqsimilar.bed

2026-05-29 00:30:00,696 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/prep_igv_seqsim_bed.ok

2026-05-29 00:30:00,698 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-05-29 00:30:00,828 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa > /tmp/nxf.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-05-29 00:30:00,828 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/add_splice_info.ok

2026-05-29 00:30:00,830 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-05-29 00:30:00,989 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.7E4AVD1Zcz/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-05-29 00:30:00,989 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/blast_filter.ok

2026-05-29 00:30:00,991 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir

2026-05-29 00:30:01,013 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir

2026-05-29 00:30:01,013 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/annot_filter.ok

2026-05-29 00:30:01,015 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-05-29 00:30:01,225 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-05-29 00:30:01,225 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/EM_adj_counts.ok

2026-05-29 00:30:01,227 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-05-29 00:35:44,931 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-05-29 00:35:44,931 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/add_FFPM.ok

2026-05-29 00:35:44,934 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --gtf /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/microH.dat

2026-05-29 00:35:46,999 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fa --gtf /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.gtf  > /tmp/nxf.7E4AVD1Zcz/fi_workdir/microH.dat

2026-05-29 00:35:46,999 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/microH.dat.ok

2026-05-29 00:35:47,002 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.7E4AVD1Zcz/fi_workdir/microH.dat /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-05-29 00:35:47,495 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.7E4AVD1Zcz/fi_workdir/microH.dat /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-05-29 00:35:47,495 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/append_microH_info.ok

2026-05-29 00:35:47,497 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv

2026-05-29 00:35:47,500 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv

2026-05-29 00:35:47,500 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/cp_final.ok

2026-05-29 00:35:47,502 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv

2026-05-29 00:35:47,518 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv

2026-05-29 00:35:47,518 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/final.abridged.ok

2026-05-29 00:35:47,520 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.7E4AVD1Zcz --json_outfile /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2

2026-05-29 00:35:47,540 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.7E4AVD1Zcz --json_outfile /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2

2026-05-29 00:35:47,540 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/create_fi_igvjs.ok

2026-05-29 00:35:47,542 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2 --html_output /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.html

2026-05-29 00:35:49,842 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_2 --html_output /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.fusion_inspector_web.html

2026-05-29 00:35:49,842 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_reports_html.ok

2026-05-29 00:35:49,844 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated 

2026-05-29 00:35:49,871 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated 

2026-05-29 00:35:49,871 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_annotator.ok

2026-05-29 00:35:49,873 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-05-29 00:35:49,960 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.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.7E4AVD1Zcz/ctat_genome_lib_build_dir > /tmp/nxf.7E4AVD1Zcz/A673_FFPE_RNA_0001_B23LG7FLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-05-29 00:35:49,961 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.7E4AVD1Zcz/chckpts_dir/fusion_coding_region_effect.ok