FusionInspector.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (GM24385_0001_RNA_0001_23H5VFLT4_s16)

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/dc39a194ad1eda093aca671a36e9e1/FusionInspector.log
Size: 44.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (GM24385_0001_RNA_0001_23H5VFLT4_s16)
Attempt
Content

2026-06-08 09:36:03,197 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions GM24385_0001_RNA_0001_23H5VFLT4_s16.fusionreport.tsv --gtf /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16 --shrink_introns --max_intron_length 1000 

2026-06-08 09:36:10,077 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions GM24385_0001_RNA_0001_23H5VFLT4_s16.fusionreport.tsv --gtf /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16 --shrink_introns --max_intron_length 1000 

2026-06-08 09:36:10,077 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/fusion_contigs.ok

2026-06-08 09:36:10,078 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa

2026-06-08 09:36:10,081 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa

2026-06-08 09:36:10,081 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/cp_contigs_file_workdir

2026-06-08 09:36:10,083 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf

2026-06-08 09:36:10,085 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf

2026-06-08 09:36:10,085 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/cp_gtf_file_workdir.ok

2026-06-08 09:36:10,087 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf > /tmp/nxf.JYUsibNMtw/cytoBand.txt

2026-06-08 09:36:10,106 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf > /tmp/nxf.JYUsibNMtw/cytoBand.txt

2026-06-08 09:36:10,106 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/cytoband.ok

2026-06-08 09:36:10,108 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed

2026-06-08 09:36:10,158 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed

2026-06-08 09:36:10,158 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-06-08 09:36:10,159 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.sorted.bed

2026-06-08 09:36:10,161 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.sorted.bed

2026-06-08 09:36:10,161 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.bedsort.ok

2026-06-08 09:36:10,163 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.sorted.bed

2026-06-08 09:36:10,169 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.sorted.bed

2026-06-08 09:36:10,169 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.bgzip.ok

2026-06-08 09:36:10,170 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.sorted.bed.gz

2026-06-08 09:36:10,175 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.sorted.bed.gz

2026-06-08 09:36:10,175 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.bed.tabix.ok

2026-06-08 09:36:10,177 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa

2026-06-08 09:36:10,182 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa

2026-06-08 09:36:10,182 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/merged_contig_fai.ok

2026-06-08 09:36:10,184 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa --max_mate_dist 100000 -G /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf --CPU 8 --out_prefix GM24385_0001_RNA_0001_23H5VFLT4_s16.star --out_dir /tmp/nxf.JYUsibNMtw/fi_workdir --reads "/tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16_1.fastp.fastq.gz /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16_2.fastp.fastq.gz"

2026-06-08 10:31:27,922 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 55.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa --max_mate_dist 100000 -G /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf --CPU 8 --out_prefix GM24385_0001_RNA_0001_23H5VFLT4_s16.star --out_dir /tmp/nxf.JYUsibNMtw/fi_workdir --reads "/tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16_1.fastp.fastq.gz /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16_2.fastp.fastq.gz"

2026-06-08 10:31:27,922 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/run_STAR.ok

2026-06-08 10:31:27,924 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.sortedByCoord.out.bam   -o /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 10:31:28,927 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.sortedByCoord.out.bam   -o /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam   --remove_dups 

2026-06-08 10:31:28,928 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/mark_dup_reads.ok

2026-06-08 10:31:28,930 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam

2026-06-08 10:31:29,052 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam

2026-06-08 10:31:29,052 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/mark_dups_reads.index.ok

2026-06-08 10:31:29,054 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 10:31:34,359 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-06-08 10:31:34,359 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-06-08 10:31:34,361 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 10:31:48,606 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-06-08 10:31:48,606 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-06-08 10:31:48,608 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary

2026-06-08 10:31:48,625 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary

2026-06-08 10:31:48,625 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/coalesce_junc_n_span.ok

2026-06-08 10:31:48,626 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj

2026-06-08 10:31:48,641 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj

2026-06-08 10:31:48,641 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/init_EM_adj_counts.ok

2026-06-08 10:31:48,643 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 10:31:48,660 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-06-08 10:31:48,660 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/filter_by_frag_threshs.ok

2026-06-08 10:31:48,662 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 10:31:48,675 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-06-08 10:31:48,675 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-06-08 10:31:48,677 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa -  | samtools sort -@ 8 - -o /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam"

2026-06-08 10:31:48,728 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa -  | samtools sort -@ 8 - -o /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam"

2026-06-08 10:31:48,729 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-06-08 10:31:48,730 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam

2026-06-08 10:31:48,735 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam

2026-06-08 10:31:48,735 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-06-08 10:31:48,737 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed

2026-06-08 10:31:48,764 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed

2026-06-08 10:31:48,764 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bam_to_bed.ok

2026-06-08 10:31:48,766 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,768 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,768 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bedsort.ok

2026-06-08 10:31:48,769 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,775 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,775 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bgzip.ok

2026-06-08 10:31:48,776 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 10:31:48,781 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.bed.sorted.bed.gz

2026-06-08 10:31:48,781 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.junction_reads.bam.tabix.ok

2026-06-08 10:31:48,783 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 10:31:48,796 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-06-08 10:31:48,796 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/span_reads_acc.ok

2026-06-08 10:31:48,798 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam

2026-06-08 10:31:48,803 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam

2026-06-08 10:31:48,803 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/init_spanning_reads_bam.ok

2026-06-08 10:31:48,805 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa -  | samtools sort -@ 8 - -o /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam || : 

2026-06-08 10:31:48,821 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa -  | samtools sort -@ 8 - -o /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam || : 

2026-06-08 10:31:48,821 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_spanning_reads.ok

2026-06-08 10:31:48,822 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam

2026-06-08 10:31:48,827 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam

2026-06-08 10:31:48,827 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/samtools_index_span_reads_bam.ok

2026-06-08 10:31:48,828 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed

2026-06-08 10:31:48,843 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed

2026-06-08 10:31:48,843 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bam_to_bed.ok

2026-06-08 10:31:48,845 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,846 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,846 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bedsort.ok

2026-06-08 10:31:48,848 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,853 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed.sorted.bed

2026-06-08 10:31:48,853 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bgzip.ok

2026-06-08 10:31:48,855 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 10:31:48,860 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.bed.sorted.bed.gz

2026-06-08 10:31:48,860 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/GM24385_0001_RNA_0001_23H5VFLT4_s16.spanning_reads.bam.tabix.ok

2026-06-08 10:31:48,861 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam

2026-06-08 10:31:48,865 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.star.cSorted.dupsMarked.bam /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam

2026-06-08 10:31:48,865 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/cp_consol_bam.ok

2026-06-08 10:31:48,867 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam

2026-06-08 10:31:48,987 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam

2026-06-08 10:31:48,987 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/index_consol_bam.ok

2026-06-08 10:31:48,989 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam --max_insert_size 10000000 

2026-06-08 10:31:51,768 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam --max_insert_size 10000000 

2026-06-08 10:31:51,768 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-06-08 10:31:51,770 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam.frag_coords > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.FusionJuncSpan

2026-06-08 10:31:51,829 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.consolidated.bam.frag_coords > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.FusionJuncSpan

2026-06-08 10:31:51,829 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-06-08 10:31:51,831 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.Pfam.gff3 

2026-06-08 10:31:51,864 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.Pfam.gff3 

2026-06-08 10:31:51,864 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_pfam_gff3.ok

2026-06-08 10:31:51,866 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.Pfam.gff3 > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.Pfam.bed

2026-06-08 10:31:51,890 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.Pfam.gff3 > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.Pfam.bed

2026-06-08 10:31:51,891 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_pfam_bed.ok

2026-06-08 10:31:51,892 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.seqsimilar.gff3 

2026-06-08 10:31:51,915 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.seqsimilar.gff3 

2026-06-08 10:31:51,915 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-06-08 10:31:51,917 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.seqsimilar.gff3 > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.seqsimilar.bed

2026-06-08 10:31:51,937 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.seqsimilar.gff3 > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.igv.seqsimilar.bed

2026-06-08 10:31:51,937 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/prep_igv_seqsim_bed.ok

2026-06-08 10:31:51,939 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 10:31:51,958 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa > /tmp/nxf.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-06-08 10:31:51,958 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/add_splice_info.ok

2026-06-08 10:31:51,960 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 10:31:52,101 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.JYUsibNMtw/fi_workdir/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-06-08 10:31:52,101 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/blast_filter.ok

2026-06-08 10:31:52,102 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir

2026-06-08 10:31:52,120 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir

2026-06-08 10:31:52,120 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/annot_filter.ok

2026-06-08 10:31:52,121 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 10:31:52,136 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-06-08 10:31:52,136 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/EM_adj_counts.ok

2026-06-08 10:31:52,138 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16_1.fastp.fastq.gz /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 10:37:25,195 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 5.55 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16_1.fastp.fastq.gz /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-06-08 10:37:25,195 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/add_FFPM.ok

2026-06-08 10:37:25,197 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa --gtf /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf  > /tmp/nxf.JYUsibNMtw/fi_workdir/microH.dat

2026-06-08 10:37:25,234 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fa --gtf /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.gtf  > /tmp/nxf.JYUsibNMtw/fi_workdir/microH.dat

2026-06-08 10:37:25,234 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/microH.dat.ok

2026-06-08 10:37:25,236 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.JYUsibNMtw/fi_workdir/microH.dat /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 10:37:25,252 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.JYUsibNMtw/fi_workdir/microH.dat /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-06-08 10:37:25,253 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/append_microH_info.ok

2026-06-08 10:37:25,254 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.tsv

2026-06-08 10:37:25,256 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.tsv

2026-06-08 10:37:25,256 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/cp_final.ok

2026-06-08 10:37:25,258 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv

2026-06-08 10:37:25,271 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv

2026-06-08 10:37:25,271 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/final.abridged.ok

2026-06-08 10:37:25,273 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.JYUsibNMtw --json_outfile /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_inspector_web.json --file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s16

2026-06-08 10:37:25,293 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.JYUsibNMtw --json_outfile /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_inspector_web.json --file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s16

2026-06-08 10:37:25,293 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/create_fi_igvjs.ok

2026-06-08 10:37:25,295 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_inspector_web.json --input_file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s16 --html_output /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_inspector_web.html

2026-06-08 10:37:25,466 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_inspector_web.json --input_file_prefix GM24385_0001_RNA_0001_23H5VFLT4_s16 --html_output /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.fusion_inspector_web.html

2026-06-08 10:37:25,467 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/fusion_reports_html.ok

2026-06-08 10:37:25,468 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 10:37:25,490 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv.annotated 

2026-06-08 10:37:25,490 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/fusion_annotator.ok

2026-06-08 10:37:25,492 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 10:37:25,523 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.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.JYUsibNMtw/ctat_genome_lib_build_dir > /tmp/nxf.JYUsibNMtw/GM24385_0001_RNA_0001_23H5VFLT4_s16.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-06-08 10:37:25,523 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.JYUsibNMtw/chckpts_dir/fusion_coding_region_effect.ok