Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/18adf10145133a025b2aacf835b23d/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/39ee7c5365d153ef7d612afc9e5fc7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/18adf10145133a025b2aacf835b23d/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/39ee7c5365d153ef7d612afc9e5fc7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/a1ef0c27e4f39cf4cdd4a6496c8982/tih_rna_sample_00680_B23MVV7LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00680_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00680_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/cytoBand.txt
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00680_B23MVV7LT4_1.star --out_dir /tmp/nxf.jJbViTbJ8s/fi_workdir --reads "/tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outSAMtype BAM SortedByCoordinate  --twopassMode None  --alignSJDBoverhangMin 10  --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705  --alignInsertionFlush Right   --alignMatesGapMax 100000  --alignIntronMax 100000  --outSAMattributes All  --readFilesIn /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:52:52 ..... started STAR run
Jun 08 10:52:52 ..... loading genome
Jun 08 10:54:35 ... generating Suffix Array index
Jun 08 10:58:29 ... completed Suffix Array index
Jun 08 10:58:30 ..... processing annotations GTF
Jun 08 10:58:30 ..... inserting junctions into the genome indices
Jun 08 10:59:31 ..... started mapping
Jun 08 11:58:38 ..... finished mapping
Jun 08 11:58:40 ..... started sorting BAM
Jun 08 11:58:41 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 65.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00680_B23MVV7LT4_1.star --out_dir /tmp/nxf.jJbViTbJ8s/fi_workdir --reads "/tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:59:01 : INFO : Done.
Execution Time = 0.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/mark_dups_reads.index.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[3200000]   -done parsing /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24,
          'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 160,
          'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 395,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 84,
          'num_hits: 9 != num_counted_on_fusion_contigs 1 ' => 11,
          'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 18,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1285,
          'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 4,
          'num genes matched < 2' => 25,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 67,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 176,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 210,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 6,
          'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 5,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 592,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
          'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 315,
          ' ** passed ** ' => 17371,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 216,
          'excessive soft clipping' => 20757,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13,
          'per_id < 96' => 18849,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 66,
          'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 264,
          'num_hits: 10 != num_counted_on_fusion_contigs 1 ' => 6,
          'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 20,
          'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 6,
          'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 4,
          'small anchor length' => 507,
          'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 20,
          'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 33,
          'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 20,
          'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
          'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 4,
          'seq-similar region overlap' => 218
        };
-writing fusion junction support info.
Execution Time = 1.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[6000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[837000]   -fusion SPANNING read extraction for scaff: ACTBP6--ACTB

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[119000]   -fusion SPANNING read extraction for scaff: ADAM9--SNTG1

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[29000]   -fusion SPANNING read extraction for scaff: ADCY9--AC010601.1

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[3000]   -fusion SPANNING read extraction for scaff: C16orf96--SEPTIN12

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[142000]   -fusion SPANNING read extraction for scaff: F13A1--NRN1

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[91000]   -fusion SPANNING read extraction for scaff: GNB1--CFAP74

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[92000]   -fusion SPANNING read extraction for scaff: GPATCH8--AL133464.1

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[91000]   
[92000]   -fusion SPANNING read extraction for scaff: GPATCH8--LINC00261

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[118000]   
[119000]   -fusion SPANNING read extraction for scaff: KATNIP--EPG5

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[48000]   
[49000]   -fusion SPANNING read extraction for scaff: KIF3B--EFCAB8

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[429000]   -fusion SPANNING read extraction for scaff: NPIPB12--AC009093.1

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[80000]   -fusion SPANNING read extraction for scaff: PATJ--AC117464.1

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[80000]   -fusion SPANNING read extraction for scaff: PATJ--LINC00971

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[10000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8

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[5000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10

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[38000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[40000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
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[6000]   
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[8000]   
[9000]   
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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[7000]   
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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[31000]   
[32000]   -fusion SPANNING read extraction for scaff: PIK3C3--RIT2

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[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
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[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[100000]   
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[102000]   
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[110000]   
[111000]   
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[115000]   
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[120000]   
[121000]   
[122000]   
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[140000]   
[141000]   
[142000]   
[143000]   
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[146000]   
[147000]   -fusion SPANNING read extraction for scaff: RIOK3--AC016074.2

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[13000]   
[14000]   
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[19000]   -fusion SPANNING read extraction for scaff: SMURF2P1--LRRC37B

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[71000]   
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[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[38000]   
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[40000]   
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[44000]   
[45000]   
[46000]   -fusion SPANNING read extraction for scaff: STX4--C16orf96

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[30000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[39000]   
[40000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[68000]   
[69000]   
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[71000]   
[72000]   
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[75000]   
[76000]   
[77000]   -fusion SPANNING read extraction for scaff: TMEM123--MMP20

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[25000]   
[26000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[69000]   
[70000]   
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[72000]   
[73000]   
[74000]   
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[77000]   
[78000]   -fusion SPANNING read extraction for scaff: USP22--C21orf62

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: ZNF528--ZNF610

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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 22010,
          'seq similar region alignment' => 62798
        };
Execution Time = 4.56 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7717.778134
EM: Round [1] log likelihood: -7717.189182
EM: Round [2] log likelihood: -7716.888387
EM: Round [3] log likelihood: -7716.624805
EM: Round [4] log likelihood: -7716.392920
EM: Round [5] log likelihood: -7716.188303
EM: Round [6] log likelihood: -7716.007244
EM: Round [7] log likelihood: -7715.846616
EM: Round [8] log likelihood: -7715.703769
EM: Round [9] log likelihood: -7715.576444
EM: Round [10] log likelihood: -7715.462705
EM: Round [11] log likelihood: -7715.360889
EM: Round [12] log likelihood: -7715.269561
EM: Round [13] log likelihood: -7715.187479
EM: Round [14] log likelihood: -7715.113565
EM: Round [15] log likelihood: -7715.046882
EM: Round [16] log likelihood: -7714.986609
EM: Round [17] log likelihood: -7714.932033
EM: Round [18] log likelihood: -7714.882526
EM: Round [19] log likelihood: -7714.837538
EM: Round [20] log likelihood: -7714.796585
EM: Round [21] log likelihood: -7714.759242
EM: Round [22] log likelihood: -7714.725132
EM: Round [23] log likelihood: -7714.693925
EM: Round [24] log likelihood: -7714.665325
EM: Round [25] log likelihood: -7714.639074
EM: Round [26] log likelihood: -7714.614941
EM: Round [27] log likelihood: -7714.592719
EM: Round [28] log likelihood: -7714.572228
EM: Round [29] log likelihood: -7714.553305
EM: Round [30] log likelihood: -7714.535803
EM: Round [31] log likelihood: -7714.519595
EM: Round [32] log likelihood: -7714.504564
EM: Round [33] log likelihood: -7714.490607
EM: Round [34] log likelihood: -7714.477630
EM: Round [35] log likelihood: -7714.465550
EM: Round [36] log likelihood: -7714.454292
EM: Round [37] log likelihood: -7714.443788
EM: Round [38] log likelihood: -7714.433976
EM: Round [39] log likelihood: -7714.424802
EM: Round [40] log likelihood: -7714.416216
EM: Round [41] log likelihood: -7714.408172
EM: Round [42] log likelihood: -7714.400629
EM: Round [43] log likelihood: -7714.393551
EM: Round [44] log likelihood: -7714.386903
EM: Round [45] log likelihood: -7714.380653
EM: Round [46] log likelihood: -7714.374775
EM: Round [47] log likelihood: -7714.369241
EM: Round [48] log likelihood: -7714.364028
EM: Round [49] log likelihood: -7714.359116
EM: Round [50] log likelihood: -7714.354482
EM: Round [51] log likelihood: -7714.350110
EM: Round [52] log likelihood: -7714.345983
EM: Round [53] log likelihood: -7714.342084
EM: Round [54] log likelihood: -7714.338399
EM: Round [55] log likelihood: -7714.334916
EM: Round [56] log likelihood: -7714.331621
EM: Round [57] log likelihood: -7714.328504
EM: Round [58] log likelihood: -7714.325553
EM: Round [59] log likelihood: -7714.322759
EM: Round [60] log likelihood: -7714.320113
EM: Round [61] log likelihood: -7714.317606
EM: Round [62] log likelihood: -7714.315230
EM: Round [63] log likelihood: -7714.312978
EM: Round [64] log likelihood: -7714.310842
EM: Round [65] log likelihood: -7714.308817
EM: Round [66] log likelihood: -7714.306896
EM: Round [67] log likelihood: -7714.305073
EM: Round [68] log likelihood: -7714.303343
EM: Round [69] log likelihood: -7714.301701
EM: Round [70] log likelihood: -7714.300142
EM: Round [71] log likelihood: -7714.298662
EM: Round [72] log likelihood: -7714.297257
EM: Round [73] log likelihood: -7714.295923
EM: Round [74] log likelihood: -7714.294655
EM: Round [75] log likelihood: -7714.293451
EM: Round [76] log likelihood: -7714.292307
EM: Round [77] log likelihood: -7714.291219
EM: Round [78] log likelihood: -7714.290187
EM: Round [79] log likelihood: -7714.289205
EM: Round [80] log likelihood: -7714.288272
EM: Round [81] log likelihood: -7714.287385
EM: Round [82] log likelihood: -7714.286542
EM: Round [83] log likelihood: -7714.285741
EM: Round [84] log likelihood: -7714.284979
EM: Round [85] log likelihood: -7714.284255
EM: Round [86] log likelihood: -7714.283566
EM: Round [87] log likelihood: -7714.282911
EM: Round [88] log likelihood: -7714.282288
EM: Round [89] log likelihood: -7714.281696
EM: Round [90] log likelihood: -7714.281133
EM: Round [91] log likelihood: -7714.280598
EM: Round [92] log likelihood: -7714.280088
EM: Round [93] log likelihood: -7714.279604
EM: Round [94] log likelihood: -7714.279143
EM: Round [95] log likelihood: -7714.278705
EM: Round [96] log likelihood: -7714.278288
EM: Round [97] log likelihood: -7714.277891
EM: Round [98] log likelihood: -7714.277514
EM: Round [99] log likelihood: -7714.277156
EM: Round [100] log likelihood: -7714.276814
EM: Round [101] log likelihood: -7714.276489
EM: Round [102] log likelihood: -7714.276181
EM: Round [103] log likelihood: -7714.275887
EM: Round [104] log likelihood: -7714.275607
EM: Round [105] log likelihood: -7714.275341
EM: Round [106] log likelihood: -7714.275088
EM: Round [107] log likelihood: -7714.274847
EM: Round [108] log likelihood: -7714.274618
EM: Round [109] log likelihood: -7714.274400
EM: Round [110] log likelihood: -7714.274193
EM: Round [111] log likelihood: -7714.273996
EM: Round [112] log likelihood: -7714.273808
EM: Round [113] log likelihood: -7714.273630
EM: Round [114] log likelihood: -7714.273460
EM: Round [115] log likelihood: -7714.273298
EM: Round [116] log likelihood: -7714.273144
EM: Round [117] log likelihood: -7714.272998
EM: Round [118] log likelihood: -7714.272859
EM: Round [119] log likelihood: -7714.272726
EM: Round [120] log likelihood: -7714.272600
EM: Round [121] log likelihood: -7714.272480
EM: Round [122] log likelihood: -7714.272366
EM: Round [123] log likelihood: -7714.272257
EM: Round [124] log likelihood: -7714.272154
EM: Round [125] log likelihood: -7714.272055
EM: Stopping iterations at round 125 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/init_EM_adj_counts.ok
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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/tih_rna_sample_00680_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_sam_frag_coordss.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_pfam_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/prep_igv_seqsim_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa > /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir
-done, see /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6772.601260
EM: Round [1] log likelihood: -6772.403710
EM: Round [2] log likelihood: -6772.403416
EM: Round [3] log likelihood: -6772.403414
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz: 296091919
Execution Time = 5.65 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa --gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf  > /tmp/nxf.jJbViTbJ8s/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fa --gtf /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf  > /tmp/nxf.jJbViTbJ8s/fi_workdir/microH.dat
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.jJbViTbJ8s/fi_workdir/microH.dat /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.jJbViTbJ8s/fi_workdir/microH.dat /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.jJbViTbJ8s --json_outfile /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00680_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.jJbViTbJ8s --json_outfile /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00680_B23MVV7LT4_1
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/create_fi_igvjs.ok
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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00680_B23MVV7LT4_1 --html_output /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00680_B23MVV7LT4_1 --html_output /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000286122.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000259929.5]
WARNING, no entry stored in dbm for [ENSG00000259929.5]
WARNING, no entry stored in dbm for [ENSG00000259807.2]
WARNING, no entry stored in dbm for [ENSG00000259807.2]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.jJbViTbJ8s/ctat_genome_lib_build_dir > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.jJbViTbJ8s/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory