File Info

Filename
FusionInspector.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/79f2ee20265826ac4851590a8a03fe/FusionInspector.log
Size
43.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (659_cRa-T1-TRNA-1_B23MHV2LT4_1)
Attempt

Content

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2026-06-08 10:05:51,460 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 10:05:59,230 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 659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 

2026-06-08 10:05:59,230 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/fusion_contigs.ok

2026-06-08 10:05:59,232 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-08 10:05:59,234 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-08 10:05:59,234 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/cp_contigs_file_workdir

2026-06-08 10:05:59,236 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf

2026-06-08 10:05:59,239 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf

2026-06-08 10:05:59,239 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 10:05:59,241 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.wXLHhalZZH/cytoBand.txt

2026-06-08 10:05:59,298 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.wXLHhalZZH/cytoBand.txt

2026-06-08 10:05:59,298 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/cytoband.ok

2026-06-08 10:05:59,300 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed

2026-06-08 10:05:59,471 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed

2026-06-08 10:05:59,471 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 10:05:59,473 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-08 10:05:59,475 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-08 10:05:59,475 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok

2026-06-08 10:05:59,477 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-08 10:05:59,488 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed

2026-06-08 10:05:59,489 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok

2026-06-08 10:05:59,490 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz

2026-06-08 10:05:59,502 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz

2026-06-08 10:05:59,502 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok

2026-06-08 10:05:59,504 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-08 10:05:59,512 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa

2026-06-08 10:05:59,512 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/merged_contig_fai.ok

2026-06-08 10:05:59,514 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_cRa-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.wXLHhalZZH/fi_workdir --reads "/tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"

2026-06-08 11:38:38,061 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 92.64 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_cRa-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.wXLHhalZZH/fi_workdir --reads "/tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"

2026-06-08 11:38:38,061 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/run_STAR.ok

2026-06-08 11:38:38,063 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:38:47,131 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 11:38:47,132 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/mark_dup_reads.ok

2026-06-08 11:38:47,134 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

2026-06-08 11:38:48,234 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

2026-06-08 11:38:48,235 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 11:38:48,237 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:39:44,575 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.94 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 11:39:44,575 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 11:39:44,578 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:42:25,927 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 2.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 11:42:25,927 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 11:42:25,929 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary

2026-06-08 11:42:25,966 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary

2026-06-08 11:42:25,966 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 11:42:25,968 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:42:26,011 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj

2026-06-08 11:42:26,011 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 11:42:26,013 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:42:26,032 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 11:42:26,033 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 11:42:26,035 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:42:26,049 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 11:42:26,049 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 11:42:26,051 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"

2026-06-08 11:42:26,127 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"

2026-06-08 11:42:26,127 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 11:42:26,129 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam

2026-06-08 11:42:26,137 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam

2026-06-08 11:42:26,138 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 11:42:26,139 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed

2026-06-08 11:42:26,246 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed

2026-06-08 11:42:26,247 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok

2026-06-08 11:42:26,248 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,252 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,252 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok

2026-06-08 11:42:26,254 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,265 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,265 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok

2026-06-08 11:42:26,267 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:42:26,274 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 11:42:26,274 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok

2026-06-08 11:42:26,276 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:42:26,290 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 11:42:26,291 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/span_reads_acc.ok

2026-06-08 11:42:26,292 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-08 11:42:26,298 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-08 11:42:26,298 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 11:42:26,299 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 

2026-06-08 11:42:26,336 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 

2026-06-08 11:42:26,336 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_spanning_reads.ok

2026-06-08 11:42:26,338 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-08 11:42:26,343 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam

2026-06-08 11:42:26,343 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 11:42:26,344 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed

2026-06-08 11:42:26,361 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed

2026-06-08 11:42:26,361 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok

2026-06-08 11:42:26,363 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,365 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,365 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok

2026-06-08 11:42:26,366 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,371 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed

2026-06-08 11:42:26,371 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok

2026-06-08 11:42:26,373 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:42:26,378 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 11:42:26,378 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok

2026-06-08 11:42:26,380 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-08 11:42:26,398 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-08 11:42:26,398 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/cp_consol_bam.ok

2026-06-08 11:42:26,400 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-08 11:42:27,533 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam

2026-06-08 11:42:27,533 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/index_consol_bam.ok

2026-06-08 11:42:27,536 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:42:53,276 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.43 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 

2026-06-08 11:42:53,277 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 11:42:53,279 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan

2026-06-08 11:42:53,765 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan

2026-06-08 11:42:53,765 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 11:42:53,767 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 

2026-06-08 11:42:53,877 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 

2026-06-08 11:42:53,877 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 11:42:53,879 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed

2026-06-08 11:42:53,929 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed

2026-06-08 11:42:53,930 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 11:42:53,931 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 

2026-06-08 11:42:53,968 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 

2026-06-08 11:42:53,968 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 11:42:53,970 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed

2026-06-08 11:42:53,990 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed

2026-06-08 11:42:53,990 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 11:42:53,992 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:42:54,037 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 11:42:54,037 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/add_splice_info.ok

2026-06-08 11:42:54,039 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:42:54,188 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.wXLHhalZZH/fi_workdir/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 11:42:54,188 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/blast_filter.ok

2026-06-08 11:42:54,190 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir

2026-06-08 11:42:54,210 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir

2026-06-08 11:42:54,210 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/annot_filter.ok

2026-06-08 11:42:54,212 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:42:54,234 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 11:42:54,234 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/EM_adj_counts.ok

2026-06-08 11:42:54,236 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:48:36,823 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.71 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 11:48:36,823 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/add_FFPM.ok

2026-06-08 11:48:36,825 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.wXLHhalZZH/fi_workdir/microH.dat

2026-06-08 11:48:36,982 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.wXLHhalZZH/fi_workdir/microH.dat

2026-06-08 11:48:36,982 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/microH.dat.ok

2026-06-08 11:48:36,984 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.wXLHhalZZH/fi_workdir/microH.dat /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:48:37,020 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.wXLHhalZZH/fi_workdir/microH.dat /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 11:48:37,020 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/append_microH_info.ok

2026-06-08 11:48:37,022 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv

2026-06-08 11:48:37,025 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv

2026-06-08 11:48:37,025 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/cp_final.ok

2026-06-08 11:48:37,026 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 11:48:37,041 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv

2026-06-08 11:48:37,041 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/final.abridged.ok

2026-06-08 11:48:37,042 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.wXLHhalZZH --json_outfile /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_cRa-T1-TRNA-1_B23MHV2LT4_1

2026-06-08 11:48:37,063 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.wXLHhalZZH --json_outfile /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_cRa-T1-TRNA-1_B23MHV2LT4_1

2026-06-08 11:48:37,063 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/create_fi_igvjs.ok

2026-06-08 11:48:37,065 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_cRa-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html

2026-06-08 11:48:37,626 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_cRa-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html

2026-06-08 11:48:37,626 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/fusion_reports_html.ok

2026-06-08 11:48:37,628 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:48:37,657 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 11:48:37,657 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/fusion_annotator.ok

2026-06-08 11:48:37,658 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:48:37,731 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.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.wXLHhalZZH/ctat_genome_lib_build_dir > /tmp/nxf.wXLHhalZZH/659_cRa-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 11:48:37,731 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.wXLHhalZZH/chckpts_dir/fusion_coding_region_effect.ok