FusionInspector.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (rna_s1221_S42)

File Info

Filename: FusionInspector.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/dd6a35681cefc54d3b2ff0485b29a2/FusionInspector.log
Size: 39.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (rna_s1221_S42)
Attempt
Content

2026-05-28 00:13:41,259 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42 --shrink_introns --max_intron_length 1000 

2026-05-28 00:13:48,220 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42 --shrink_introns --max_intron_length 1000 

2026-05-28 00:13:48,221 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/fusion_contigs.ok

2026-05-28 00:13:48,222 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fa

2026-05-28 00:13:48,224 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fa

2026-05-28 00:13:48,224 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/cp_contigs_file_workdir

2026-05-28 00:13:48,225 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf

2026-05-28 00:13:48,228 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf

2026-05-28 00:13:48,228 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/cp_gtf_file_workdir.ok

2026-05-28 00:13:48,229 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf > /tmp/nxf.Bfq1tnqHDv/cytoBand.txt

2026-05-28 00:13:48,264 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.Bfq1tnqHDv/rna_s1221_S42.fa /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf > /tmp/nxf.Bfq1tnqHDv/cytoBand.txt

2026-05-28 00:13:48,264 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/cytoband.ok

2026-05-28 00:13:48,266 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed

2026-05-28 00:13:48,366 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.Bfq1tnqHDv/rna_s1221_S42.gtf > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed

2026-05-28 00:13:48,366 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/merged_contig_gtf_to_bed.ok

2026-05-28 00:13:48,367 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed.sorted.bed

2026-05-28 00:13:48,369 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed.sorted.bed

2026-05-28 00:13:48,369 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.bed.bedsort.ok

2026-05-28 00:13:48,371 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed.sorted.bed

2026-05-28 00:13:48,389 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed.sorted.bed

2026-05-28 00:13:48,389 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.bed.bgzip.ok

2026-05-28 00:13:48,391 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed.sorted.bed.gz

2026-05-28 00:13:48,407 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.bed.sorted.bed.gz

2026-05-28 00:13:48,408 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.bed.tabix.ok

2026-05-28 00:13:48,409 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools faidx /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa

2026-05-28 00:13:48,415 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa

2026-05-28 00:13:48,415 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/merged_contig_fai.ok

2026-05-28 00:13:48,417 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.Bfq1tnqHDv/fi_workdir --reads "/tmp/nxf.Bfq1tnqHDv/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42_2.fastp.fastq.gz"

2026-05-28 00:21:41,405 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 7.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf --CPU 8 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.Bfq1tnqHDv/fi_workdir --reads "/tmp/nxf.Bfq1tnqHDv/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42_2.fastp.fastq.gz"

2026-05-28 00:21:41,405 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/run_STAR.ok

2026-05-28 00:21:41,407 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam   -o /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam   --remove_dups 

2026-05-28 00:21:41,773 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam   -o /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam   --remove_dups 

2026-05-28 00:21:41,773 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/mark_dup_reads.ok

2026-05-28 00:21:41,775 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam

2026-05-28 00:21:41,819 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam

2026-05-28 00:21:41,819 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/mark_dups_reads.index.ok

2026-05-28 00:21:41,821 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-05-28 00:21:43,479 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam

2026-05-28 00:21:43,479 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok

2026-05-28 00:21:43,482 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-05-28 00:21:48,814 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam

2026-05-28 00:21:48,815 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok

2026-05-28 00:21:48,817 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary

2026-05-28 00:21:48,832 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary

2026-05-28 00:21:48,832 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/coalesce_junc_n_span.ok

2026-05-28 00:21:48,834 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj

2026-05-28 00:21:48,847 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj

2026-05-28 00:21:48,848 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/init_EM_adj_counts.ok

2026-05-28 00:21:48,849 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-05-28 00:21:48,867 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh

2026-05-28 00:21:48,867 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/filter_by_frag_threshs.ok

2026-05-28 00:21:48,868 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-05-28 00:21:48,881 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs

2026-05-28 00:21:48,881 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_extract_junc_reads.ok

2026-05-28 00:21:48,882 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam"

2026-05-28 00:21:48,922 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam"

2026-05-28 00:21:48,922 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_junc_reads_bam.ok

2026-05-28 00:21:48,924 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam

2026-05-28 00:21:48,929 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam

2026-05-28 00:21:48,929 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/samtools_idx_junc_reads_bam.ok

2026-05-28 00:21:48,930 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed

2026-05-28 00:21:48,952 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.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed

2026-05-28 00:21:48,952 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.junction_reads.bam.bam_to_bed.ok

2026-05-28 00:21:48,953 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-05-28 00:21:48,955 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-05-28 00:21:48,955 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.junction_reads.bam.bedsort.ok

2026-05-28 00:21:48,957 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-05-28 00:21:48,963 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed.sorted.bed

2026-05-28 00:21:48,963 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.junction_reads.bam.bgzip.ok

2026-05-28 00:21:48,965 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz

2026-05-28 00:21:48,970 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz

2026-05-28 00:21:48,970 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.junction_reads.bam.tabix.ok

2026-05-28 00:21:48,972 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-05-28 00:21:48,984 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs

2026-05-28 00:21:48,984 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/span_reads_acc.ok

2026-05-28 00:21:48,986 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools view -H /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam

2026-05-28 00:21:48,991 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam

2026-05-28 00:21:48,991 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/init_spanning_reads_bam.ok

2026-05-28 00:21:48,992 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam || : 

2026-05-28 00:21:49,028 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam || : 

2026-05-28 00:21:49,028 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_spanning_reads.ok

2026-05-28 00:21:49,029 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam

2026-05-28 00:21:49,033 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam

2026-05-28 00:21:49,034 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/samtools_index_span_reads_bam.ok

2026-05-28 00:21:49,035 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed

2026-05-28 00:21:49,049 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.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed

2026-05-28 00:21:49,049 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bam_to_bed.ok

2026-05-28 00:21:49,051 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: sort -k1,1 -k2,2n /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-05-28 00:21:49,052 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-05-28 00:21:49,053 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bedsort.ok

2026-05-28 00:21:49,054 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: bgzip -f /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-05-28 00:21:49,059 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed

2026-05-28 00:21:49,059 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bgzip.ok

2026-05-28 00:21:49,060 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: tabix -p bed /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz

2026-05-28 00:21:49,065 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz

2026-05-28 00:21:49,065 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/rna_s1221_S42.spanning_reads.bam.tabix.ok

2026-05-28 00:21:49,067 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam

2026-05-28 00:21:49,069 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam

2026-05-28 00:21:49,069 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/cp_consol_bam.ok

2026-05-28 00:21:49,071 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: samtools index /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam

2026-05-28 00:21:49,113 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam

2026-05-28 00:21:49,113 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/index_consol_bam.ok

2026-05-28 00:21:49,114 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 

2026-05-28 00:21:49,960 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 

2026-05-28 00:21:49,960 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_sam_frag_coordss.ok

2026-05-28 00:21:49,962 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.FusionJuncSpan

2026-05-28 00:21:49,988 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.FusionJuncSpan

2026-05-28 00:21:49,988 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_juncspan_fmt.ok

2026-05-28 00:21:49,990 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.Pfam.gff3 

2026-05-28 00:21:50,063 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.Bfq1tnqHDv/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.Pfam.gff3 

2026-05-28 00:21:50,063 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_pfam_gff3.ok

2026-05-28 00:21:50,065 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.Pfam.bed

2026-05-28 00:21:50,103 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.Bfq1tnqHDv/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.Pfam.bed

2026-05-28 00:21:50,103 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_pfam_bed.ok

2026-05-28 00:21:50,105 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.Bfq1tnqHDv/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.seqsimilar.gff3 

2026-05-28 00:21:50,133 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.Bfq1tnqHDv/rna_s1221_S42.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.seqsimilar.gff3 

2026-05-28 00:21:50,133 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_seqsim_gff3.ok

2026-05-28 00:21:50,135 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.seqsimilar.bed

2026-05-28 00:21:50,155 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.Bfq1tnqHDv/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.igv.seqsimilar.bed

2026-05-28 00:21:50,155 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/prep_igv_seqsim_bed.ok

2026-05-28 00:21:50,157 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-05-28 00:21:50,186 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fa > /tmp/nxf.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo

2026-05-28 00:21:50,186 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/add_splice_info.ok

2026-05-28 00:21:50,187 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-05-28 00:21:50,334 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.Bfq1tnqHDv/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50

2026-05-28 00:21:50,334 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/blast_filter.ok

2026-05-28 00:21:50,335 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.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir

2026-05-28 00:21:50,353 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.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir

2026-05-28 00:21:50,353 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/annot_filter.ok

2026-05-28 00:21:50,355 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-05-28 00:21:50,369 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.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj

2026-05-28 00:21:50,369 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/EM_adj_counts.ok

2026-05-28 00:21:50,370 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-05-28 00:22:03,215 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM

2026-05-28 00:22:03,215 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/add_FFPM.ok

2026-05-28 00:22:03,217 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.Bfq1tnqHDv/rna_s1221_S42.fa --gtf /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/microH.dat

2026-05-28 00:22:03,300 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.Bfq1tnqHDv/rna_s1221_S42.fa --gtf /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.gtf  > /tmp/nxf.Bfq1tnqHDv/fi_workdir/microH.dat

2026-05-28 00:22:03,300 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/microH.dat.ok

2026-05-28 00:22:03,302 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Bfq1tnqHDv/fi_workdir/microH.dat /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-05-28 00:22:03,321 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.Bfq1tnqHDv/fi_workdir/microH.dat /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH

2026-05-28 00:22:03,321 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/append_microH_info.ok

2026-05-28 00:22:03,323 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: cp /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.tsv

2026-05-28 00:22:03,325 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.tsv

2026-05-28 00:22:03,325 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/cp_final.ok

2026-05-28 00:22:03,326 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv

2026-05-28 00:22:03,339 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv

2026-05-28 00:22:03,339 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/final.abridged.ok

2026-05-28 00:22:03,341 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.Bfq1tnqHDv --json_outfile /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42

2026-05-28 00:22:03,362 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.Bfq1tnqHDv --json_outfile /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42

2026-05-28 00:22:03,362 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/create_fi_igvjs.ok

2026-05-28 00:22:03,364 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.Bfq1tnqHDv/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fusion_inspector_web.html

2026-05-28 00:22:03,741 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.Bfq1tnqHDv/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.fusion_inspector_web.html

2026-05-28 00:22:03,741 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/fusion_reports_html.ok

2026-05-28 00:22:03,743 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 

2026-05-28 00:22:03,768 INFO Pipeliner.Pipeliner.run at 136 :
	Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 

2026-05-28 00:22:03,768 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/fusion_annotator.ok

2026-05-28 00:22:03,770 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.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-05-28 00:22:03,831 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.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Bfq1tnqHDv/ctat_genome_lib_build_dir > /tmp/nxf.Bfq1tnqHDv/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 

2026-05-28 00:22:03,831 INFO Pipeliner.Pipeliner.run_cmd at 21 :
	Running: touch /tmp/nxf.Bfq1tnqHDv/chckpts_dir/fusion_coding_region_effect.ok