Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/174b185e6eea6e81bfe906b589510f/tih_rna_sample_00118_23H5VFLT4_s38_2.fastp.fastq.gz
  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/db/7151ba8f0eb992de79379165a18080/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/7151ba8f0eb992de79379165a18080/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/565b258447644ffc58cab41e29ce0e/tih_rna_sample_00118_23H5VFLT4_s38.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/174b185e6eea6e81bfe906b589510f/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00118_23H5VFLT4_s38.fusionreport.tsv --gtf /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00118_23H5VFLT4_s38.fusionreport.tsv --gtf /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fa
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf > /tmp/nxf.Gxw6aZN623/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf > /tmp/nxf.Gxw6aZN623/cytoBand.txt
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed
-parsing GTF file: /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed.sorted.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed.sorted.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.bed.sorted.bed.gz
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.bed.tabix.ok
Running: samtools faidx /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fa --max_mate_dist 100000 -G /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf --CPU 8 --out_prefix tih_rna_sample_00118_23H5VFLT4_s38.star --out_dir /tmp/nxf.Gxw6aZN623/fi_workdir --reads "/tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:30:55 ..... started STAR run
Jun 08 09:30:55 ..... loading genome
Jun 08 09:32:40 ... generating Suffix Array index
Jun 08 09:36:37 ... completed Suffix Array index
Jun 08 09:36:37 ..... processing annotations GTF
Jun 08 09:36:37 ..... inserting junctions into the genome indices
Jun 08 09:37:39 ..... started mapping
Jun 08 10:35:54 ..... finished mapping
Jun 08 10:35:55 ..... started sorting BAM
Jun 08 10:35:56 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00118_23H5VFLT4_s38.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00118_23H5VFLT4_s38.star.sortedByCoord.out.bam
Execution Time = 65.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fa --max_mate_dist 100000 -G /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf --CPU 8 --out_prefix tih_rna_sample_00118_23H5VFLT4_s38.star --out_dir /tmp/nxf.Gxw6aZN623/fi_workdir --reads "/tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_2.fastp.fastq.gz"
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.sortedByCoord.out.bam   -o /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam   --remove_dups 
10:36:04 : INFO : Done.
Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.sortedByCoord.out.bam   -o /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf
-parsing /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam

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[1180000]   -done parsing /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 8311,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 20,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 18,
          'seq-similar region overlap' => 255,
          'num genes matched < 2' => 10,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
          'excessive soft clipping' => 8971,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 95,
          'small anchor length' => 19,
          'exons hit < 2' => 5,
          'per_id < 96' => 3520
        };
-writing fusion junction support info.
Execution Time = 0.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[13000]   -fusion SPANNING read extraction for scaff: MTA3--PLEKHH2

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[5000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[5000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[7000]   
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[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[57000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
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[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PPP4R3A--AL133373.1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PTPN20--BMS1P7

[1000]   
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[6000]   
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[16000]   
[17000]   
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[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: RAP1GDS1--STPG2

[1000]   
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[8000]   
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[20000]   
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[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: RAP1GDS1--AC019077.1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[13000]   
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[20000]   
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[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: SLCO1B3--SLCO1B7

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[12000]   
[13000]   
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[30000]   
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[33000]   
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[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
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[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   -fusion SPANNING read extraction for scaff: SPATA13--AL159978.1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[13000]   
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[20000]   
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[30000]   
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[35000]   
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[37000]   
[38000]   
[39000]   
[40000]   
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[44000]   
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[48000]   
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[50000]   
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[53000]   
[54000]   
[55000]   
[56000]   
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[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
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[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   -fusion SPANNING read extraction for scaff: SPATA13--GPR12

[1000]   
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[9000]   
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[30000]   
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[42000]   
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[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   -fusion SPANNING read extraction for scaff: SPATA13--FGFR1OP2P1

[1000]   
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[8000]   
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[14000]   
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[26000]   
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[40000]   
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[42000]   
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[50000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[12000]   
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[20000]   
[21000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
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[20000]   
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[30000]   
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[32000]   
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[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
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[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
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[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   -fusion SPANNING read extraction for scaff: TM9SF2--CLYBL

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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[6000]   
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[8000]   
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[13000]   
[14000]   
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[20000]   
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[30000]   
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[62000]   
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[64000]   
[65000]   
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[69000]   
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[71000]   
[72000]   
[73000]   
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[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   -fusion SPANNING read extraction for scaff: UBAC2--TM9SF2

[1000]   
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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: VPS26B--PTPN20

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: VPS26B--GDF10

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: ZNF419--ZNF772
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 56273,
          'lacks exon overlap' => 14385
        };
Execution Time = 1.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6238.480830
EM: Round [1] log likelihood: -6238.249744
EM: Round [2] log likelihood: -6238.235409
EM: Round [3] log likelihood: -6238.223195
EM: Round [4] log likelihood: -6238.211483
EM: Round [5] log likelihood: -6238.200226
EM: Round [6] log likelihood: -6238.189402
EM: Round [7] log likelihood: -6238.178990
EM: Round [8] log likelihood: -6238.168970
EM: Round [9] log likelihood: -6238.159323
EM: Round [10] log likelihood: -6238.150033
EM: Round [11] log likelihood: -6238.141083
EM: Round [12] log likelihood: -6238.132458
EM: Round [13] log likelihood: -6238.124143
EM: Round [14] log likelihood: -6238.116125
EM: Round [15] log likelihood: -6238.108390
EM: Round [16] log likelihood: -6238.100928
EM: Round [17] log likelihood: -6238.093725
EM: Round [18] log likelihood: -6238.086773
EM: Round [19] log likelihood: -6238.080059
EM: Round [20] log likelihood: -6238.073575
EM: Round [21] log likelihood: -6238.067310
EM: Round [22] log likelihood: -6238.061258
EM: Round [23] log likelihood: -6238.055408
EM: Round [24] log likelihood: -6238.049754
EM: Round [25] log likelihood: -6238.044287
EM: Round [26] log likelihood: -6238.039000
EM: Round [27] log likelihood: -6238.033887
EM: Round [28] log likelihood: -6238.028941
EM: Round [29] log likelihood: -6238.024155
EM: Round [30] log likelihood: -6238.019525
EM: Round [31] log likelihood: -6238.015043
EM: Round [32] log likelihood: -6238.010705
EM: Round [33] log likelihood: -6238.006506
EM: Round [34] log likelihood: -6238.002440
EM: Round [35] log likelihood: -6237.998503
EM: Round [36] log likelihood: -6237.994690
EM: Round [37] log likelihood: -6237.990996
EM: Round [38] log likelihood: -6237.987419
EM: Round [39] log likelihood: -6237.983953
EM: Round [40] log likelihood: -6237.980594
EM: Round [41] log likelihood: -6237.977340
EM: Round [42] log likelihood: -6237.974187
EM: Round [43] log likelihood: -6237.971130
EM: Round [44] log likelihood: -6237.968167
EM: Round [45] log likelihood: -6237.965295
EM: Round [46] log likelihood: -6237.962511
EM: Round [47] log likelihood: -6237.959811
EM: Round [48] log likelihood: -6237.957194
EM: Round [49] log likelihood: -6237.954655
EM: Round [50] log likelihood: -6237.952193
EM: Round [51] log likelihood: -6237.949806
EM: Round [52] log likelihood: -6237.947490
EM: Round [53] log likelihood: -6237.945244
EM: Round [54] log likelihood: -6237.943065
EM: Round [55] log likelihood: -6237.940951
EM: Round [56] log likelihood: -6237.938900
EM: Round [57] log likelihood: -6237.936910
EM: Round [58] log likelihood: -6237.934979
EM: Round [59] log likelihood: -6237.933105
EM: Round [60] log likelihood: -6237.931287
EM: Round [61] log likelihood: -6237.929522
EM: Round [62] log likelihood: -6237.927809
EM: Round [63] log likelihood: -6237.926147
EM: Round [64] log likelihood: -6237.924534
EM: Round [65] log likelihood: -6237.922967
EM: Round [66] log likelihood: -6237.921447
EM: Round [67] log likelihood: -6237.919971
EM: Round [68] log likelihood: -6237.918538
EM: Round [69] log likelihood: -6237.917147
EM: Round [70] log likelihood: -6237.915797
EM: Round [71] log likelihood: -6237.914486
EM: Round [72] log likelihood: -6237.913212
EM: Round [73] log likelihood: -6237.911976
EM: Round [74] log likelihood: -6237.910776
EM: Round [75] log likelihood: -6237.909610
EM: Round [76] log likelihood: -6237.908478
EM: Round [77] log likelihood: -6237.907378
EM: Round [78] log likelihood: -6237.906311
EM: Round [79] log likelihood: -6237.905274
EM: Round [80] log likelihood: -6237.904267
EM: Round [81] log likelihood: -6237.903289
EM: Round [82] log likelihood: -6237.902339
EM: Round [83] log likelihood: -6237.901416
EM: Round [84] log likelihood: -6237.900519
EM: Round [85] log likelihood: -6237.899649
EM: Round [86] log likelihood: -6237.898803
EM: Round [87] log likelihood: -6237.897981
EM: Round [88] log likelihood: -6237.897183
EM: Round [89] log likelihood: -6237.896408
EM: Round [90] log likelihood: -6237.895654
EM: Round [91] log likelihood: -6237.894923
EM: Round [92] log likelihood: -6237.894212
EM: Round [93] log likelihood: -6237.893521
EM: Round [94] log likelihood: -6237.892850
EM: Round [95] log likelihood: -6237.892198
EM: Round [96] log likelihood: -6237.891565
EM: Round [97] log likelihood: -6237.890949
EM: Round [98] log likelihood: -6237.890351
EM: Round [99] log likelihood: -6237.889770
EM: Round [100] log likelihood: -6237.889205
EM: Round [101] log likelihood: -6237.888657
EM: Round [102] log likelihood: -6237.888124
EM: Round [103] log likelihood: -6237.887606
EM: Round [104] log likelihood: -6237.887102
EM: Round [105] log likelihood: -6237.886613
EM: Round [106] log likelihood: -6237.886138
EM: Round [107] log likelihood: -6237.885676
EM: Round [108] log likelihood: -6237.885227
EM: Round [109] log likelihood: -6237.884791
EM: Round [110] log likelihood: -6237.884367
EM: Round [111] log likelihood: -6237.883955
EM: Round [112] log likelihood: -6237.883555
EM: Round [113] log likelihood: -6237.883165
EM: Round [114] log likelihood: -6237.882787
EM: Round [115] log likelihood: -6237.882420
EM: Round [116] log likelihood: -6237.882063
EM: Round [117] log likelihood: -6237.881716
EM: Round [118] log likelihood: -6237.881378
EM: Round [119] log likelihood: -6237.881050
EM: Round [120] log likelihood: -6237.880732
EM: Round [121] log likelihood: -6237.880422
EM: Round [122] log likelihood: -6237.880121
EM: Round [123] log likelihood: -6237.879828
EM: Round [124] log likelihood: -6237.879544
EM: Round [125] log likelihood: -6237.879268
EM: Round [126] log likelihood: -6237.878999
EM: Round [127] log likelihood: -6237.878738
EM: Round [128] log likelihood: -6237.878484
EM: Round [129] log likelihood: -6237.878238
EM: Round [130] log likelihood: -6237.877998
EM: Round [131] log likelihood: -6237.877765
EM: Round [132] log likelihood: -6237.877538
EM: Round [133] log likelihood: -6237.877318
EM: Round [134] log likelihood: -6237.877104
EM: Round [135] log likelihood: -6237.876896
EM: Round [136] log likelihood: -6237.876694
EM: Round [137] log likelihood: -6237.876497
EM: Round [138] log likelihood: -6237.876306
EM: Round [139] log likelihood: -6237.876120
EM: Round [140] log likelihood: -6237.875940
EM: Round [141] log likelihood: -6237.875764
EM: Round [142] log likelihood: -6237.875594
EM: Round [143] log likelihood: -6237.875428
EM: Round [144] log likelihood: -6237.875267
EM: Round [145] log likelihood: -6237.875110
EM: Round [146] log likelihood: -6237.874958
EM: Round [147] log likelihood: -6237.874810
EM: Round [148] log likelihood: -6237.874666
EM: Round [149] log likelihood: -6237.874526
EM: Round [150] log likelihood: -6237.874390
EM: Round [151] log likelihood: -6237.874258
EM: Round [152] log likelihood: -6237.874129
EM: Round [153] log likelihood: -6237.874004
EM: Round [154] log likelihood: -6237.873883
EM: Round [155] log likelihood: -6237.873765
EM: Round [156] log likelihood: -6237.873650
EM: Round [157] log likelihood: -6237.873539
EM: Round [158] log likelihood: -6237.873430
EM: Round [159] log likelihood: -6237.873325
EM: Round [160] log likelihood: -6237.873222
EM: Round [161] log likelihood: -6237.873123
EM: Stopping iterations at round 161 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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam"
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam || : 
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/tih_rna_sample_00118_23H5VFLT4_s38.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam into /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.frag_coords > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.frag_coords > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.frag_coords > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.FusionJuncSpan
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.Pfam.gff3 
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.Pfam.gff3 > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.Pfam.gff3 > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.Pfam.bed
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.seqsimilar.gff3 > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.seqsimilar.gff3 > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.igv.seqsimilar.bed
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa > /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38 --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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5999.148165
EM: Round [1] log likelihood: -5999.100045
EM: Round [2] log likelihood: -5999.099520
EM: Round [3] log likelihood: -5999.099506
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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz: 296764304
Execution Time = 5.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa --gtf /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf  > /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fa --gtf /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf  > /tmp/nxf.Gxw6aZN623/fi_workdir/microH.dat
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Gxw6aZN623/fi_workdir/microH.dat /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/microH.dat /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Gxw6aZN623 --json_outfile /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fusion_inspector_web.json --file_prefix tih_rna_sample_00118_23H5VFLT4_s38
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Gxw6aZN623 --json_outfile /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fusion_inspector_web.json --file_prefix tih_rna_sample_00118_23H5VFLT4_s38
Running: touch /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00118_23H5VFLT4_s38 --html_output /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gmap_trinity_GG.fusions.gff3.bed
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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00118_23H5VFLT4_s38 --html_output /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.fusion_inspector_web.html
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
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 [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Gxw6aZN623/ctat_genome_lib_build_dir > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.Gxw6aZN623/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory