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/f5/36c46edf01a4842ba0cec0c0b0e740/tih_rna_sample_00758_B23MVV7LT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/acaf751dfa9b41e7dc3fcdb4e8fdb5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/8d270f87a8ceef802e3b0a1137a19a/tih_rna_sample_00758_B23MVV7LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/acaf751dfa9b41e7dc3fcdb4e8fdb5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/8d270f87a8ceef802e3b0a1137a19a/tih_rna_sample_00758_B23MVV7LT4_1_2.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_00758_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1 --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_00758_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf > /tmp/nxf.9BllnXalgH/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf > /tmp/nxf.9BllnXalgH/cytoBand.txt
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00758_B23MVV7LT4_1.star --out_dir /tmp/nxf.9BllnXalgH/fi_workdir --reads "/tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.9BllnXalgH/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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:09:50 ..... started STAR run
Jun 08 10:09:50 ..... loading genome
Jun 08 10:11:32 ... generating Suffix Array index
Jun 08 10:15:25 ... completed Suffix Array index
Jun 08 10:15:25 ..... processing annotations GTF
Jun 08 10:15:26 ..... inserting junctions into the genome indices
Jun 08 10:16:27 ..... started mapping
Jun 08 11:39:06 ..... finished mapping
Jun 08 11:39:07 ..... started sorting BAM
Jun 08 11:39:08 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00758_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00758_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 89.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00758_B23MVV7LT4_1.star --out_dir /tmp/nxf.9BllnXalgH/fi_workdir --reads "/tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:39:19 : INFO : Done.
Execution Time = 0.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1810000]   -done parsing /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
          'exons hit < 2' => 3,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
          'num genes matched < 2' => 43,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 6,
          'per_id < 96' => 5315,
          ' ** passed ** ' => 6254,
          'excessive soft clipping' => 9315,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 21,
          'small anchor length' => 27,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 30,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10,
          'seq-similar region overlap' => 411,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 208
        };
-writing fusion junction support info.
Execution Time = 0.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[14000]   -fusion SPANNING read extraction for scaff: AC079781.4--ASNS

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[13000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[619000]   
[620000]   
[621000]   
[622000]   
[623000]   
[624000]   
[625000]   -fusion SPANNING read extraction for scaff: ACTBP6--ACTB

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
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[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   -fusion SPANNING read extraction for scaff: BAG4--PIGL

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

[1000]   
[2000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[87000]   
[88000]   
[89000]   -fusion SPANNING read extraction for scaff: GUSBP13--NAIP

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: LHFPL5--CLPSL1

[1000]   
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[169000]   
[170000]   -fusion SPANNING read extraction for scaff: NSD3--CSH1

[1000]   
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[169000]   
[170000]   -fusion SPANNING read extraction for scaff: NSD3--CSH2

[1000]   
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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PBX3--AHCYP2

[1000]   
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[51000]   
[52000]   -fusion SPANNING read extraction for scaff: PBX3--FBXW2

[1000]   
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[6000]   
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[8000]   
[9000]   
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[20000]   
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[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
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[6000]   
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[8000]   
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[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
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[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

[1000]   
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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

[1000]   
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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[6000]   
[7000]   
[8000]   
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[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[6000]   
[7000]   
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[30000]   
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[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[6000]   
[7000]   
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[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
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[6000]   
[7000]   
[8000]   
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[20000]   
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[25000]   
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[30000]   
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[40000]   
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[50000]   
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[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[8000]   
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[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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

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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 20477,
          'seq similar region alignment' => 61596
        };
Execution Time = 2.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -5266.279159
EM: Round [1] log likelihood: -5255.317209
EM: Round [2] log likelihood: -5251.813725
EM: Round [3] log likelihood: -5250.232887
EM: Round [4] log likelihood: -5249.318824
EM: Round [5] log likelihood: -5248.679242
EM: Round [6] log likelihood: -5248.175969
EM: Round [7] log likelihood: -5247.753953
EM: Round [8] log likelihood: -5247.388130
EM: Round [9] log likelihood: -5247.065378
EM: Round [10] log likelihood: -5246.777818
EM: Round [11] log likelihood: -5246.520111
EM: Round [12] log likelihood: -5246.288280
EM: Round [13] log likelihood: -5246.079160
EM: Round [14] log likelihood: -5245.890131
EM: Round [15] log likelihood: -5245.718960
EM: Round [16] log likelihood: -5245.563717
EM: Round [17] log likelihood: -5245.422721
EM: Round [18] log likelihood: -5245.294490
EM: Round [19] log likelihood: -5245.177722
EM: Round [20] log likelihood: -5245.071259
EM: Round [21] log likelihood: -5244.974077
EM: Round [22] log likelihood: -5244.885262
EM: Round [23] log likelihood: -5244.804000
EM: Round [24] log likelihood: -5244.729565
EM: Round [25] log likelihood: -5244.661306
EM: Round [26] log likelihood: -5244.598640
EM: Round [27] log likelihood: -5244.541045
EM: Round [28] log likelihood: -5244.488051
EM: Round [29] log likelihood: -5244.439236
EM: Round [30] log likelihood: -5244.394220
EM: Round [31] log likelihood: -5244.352660
EM: Round [32] log likelihood: -5244.314248
EM: Round [33] log likelihood: -5244.278704
EM: Round [34] log likelihood: -5244.245777
EM: Round [35] log likelihood: -5244.215238
EM: Round [36] log likelihood: -5244.186881
EM: Round [37] log likelihood: -5244.160519
EM: Round [38] log likelihood: -5244.135982
EM: Round [39] log likelihood: -5244.113117
EM: Round [40] log likelihood: -5244.091783
EM: Round [41] log likelihood: -5244.071855
EM: Round [42] log likelihood: -5244.053216
EM: Round [43] log likelihood: -5244.035762
EM: Round [44] log likelihood: -5244.019398
EM: Round [45] log likelihood: -5244.004035
EM: Round [46] log likelihood: -5243.989595
EM: Round [47] log likelihood: -5243.976005
EM: Round [48] log likelihood: -5243.963200
EM: Round [49] log likelihood: -5243.951118
EM: Round [50] log likelihood: -5243.939705
EM: Round [51] log likelihood: -5243.928910
EM: Round [52] log likelihood: -5243.918688
EM: Round [53] log likelihood: -5243.908995
EM: Round [54] log likelihood: -5243.899793
EM: Round [55] log likelihood: -5243.891047
EM: Round [56] log likelihood: -5243.882724
EM: Round [57] log likelihood: -5243.874795
EM: Round [58] log likelihood: -5243.867231
EM: Round [59] log likelihood: -5243.860007
EM: Round [60] log likelihood: -5243.853101
EM: Round [61] log likelihood: -5243.846491
EM: Round [62] log likelihood: -5243.840157
EM: Round [63] log likelihood: -5243.834081
EM: Round [64] log likelihood: -5243.828247
EM: Round [65] log likelihood: -5243.822638
EM: Round [66] log likelihood: -5243.817242
EM: Round [67] log likelihood: -5243.812045
EM: Round [68] log likelihood: -5243.807034
EM: Round [69] log likelihood: -5243.802199
EM: Round [70] log likelihood: -5243.797529
EM: Round [71] log likelihood: -5243.793014
EM: Round [72] log likelihood: -5243.788646
EM: Round [73] log likelihood: -5243.784416
EM: Round [74] log likelihood: -5243.780317
EM: Round [75] log likelihood: -5243.776341
EM: Round [76] log likelihood: -5243.772483
EM: Round [77] log likelihood: -5243.768735
EM: Round [78] log likelihood: -5243.765092
EM: Round [79] log likelihood: -5243.761550
EM: Round [80] log likelihood: -5243.758102
EM: Round [81] log likelihood: -5243.754744
EM: Round [82] log likelihood: -5243.751473
EM: Round [83] log likelihood: -5243.748283
EM: Round [84] log likelihood: -5243.745172
EM: Round [85] log likelihood: -5243.742136
EM: Round [86] log likelihood: -5243.739170
EM: Round [87] log likelihood: -5243.736274
EM: Round [88] log likelihood: -5243.733443
EM: Round [89] log likelihood: -5243.730674
EM: Round [90] log likelihood: -5243.727966
EM: Round [91] log likelihood: -5243.725316
EM: Round [92] log likelihood: -5243.722721
EM: Round [93] log likelihood: -5243.720181
EM: Round [94] log likelihood: -5243.717691
EM: Round [95] log likelihood: -5243.715252
EM: Round [96] log likelihood: -5243.712860
EM: Round [97] log likelihood: -5243.710515
EM: Round [98] log likelihood: -5243.708215
EM: Round [99] log likelihood: -5243.705958
EM: Round [100] log likelihood: -5243.703743
EM: Round [101] log likelihood: -5243.701568
EM: Round [102] log likelihood: -5243.699433
EM: Round [103] log likelihood: -5243.697336
EM: Round [104] log likelihood: -5243.695276
EM: Round [105] log likelihood: -5243.693252
EM: Round [106] log likelihood: -5243.691263
EM: Round [107] log likelihood: -5243.689308
EM: Round [108] log likelihood: -5243.687386
EM: Round [109] log likelihood: -5243.685496
EM: Round [110] log likelihood: -5243.683638
EM: Round [111] log likelihood: -5243.681810
EM: Round [112] log likelihood: -5243.680012
EM: Round [113] log likelihood: -5243.678243
EM: Round [114] log likelihood: -5243.676502
EM: Round [115] log likelihood: -5243.674789
EM: Round [116] log likelihood: -5243.673103
EM: Round [117] log likelihood: -5243.671443
EM: Round [118] log likelihood: -5243.669810
EM: Round [119] log likelihood: -5243.668201
EM: Round [120] log likelihood: -5243.666617
EM: Round [121] log likelihood: -5243.665057
EM: Round [122] log likelihood: -5243.663521
EM: Round [123] log likelihood: -5243.662009
EM: Round [124] log likelihood: -5243.660518
EM: Round [125] log likelihood: -5243.659051
EM: Round [126] log likelihood: -5243.657604
EM: Round [127] log likelihood: -5243.656180
EM: Round [128] log likelihood: -5243.654776
EM: Round [129] log likelihood: -5243.653393
EM: Round [130] log likelihood: -5243.652030
EM: Round [131] log likelihood: -5243.650686
EM: Round [132] log likelihood: -5243.649363
EM: Round [133] log likelihood: -5243.648058
EM: Round [134] log likelihood: -5243.646772
EM: Round [135] log likelihood: -5243.645504
EM: Round [136] log likelihood: -5243.644255
EM: Round [137] log likelihood: -5243.643023
EM: Round [138] log likelihood: -5243.641809
EM: Round [139] log likelihood: -5243.640612
EM: Round [140] log likelihood: -5243.639431
EM: Round [141] log likelihood: -5243.638268
EM: Round [142] log likelihood: -5243.637120
EM: Round [143] log likelihood: -5243.635989
EM: Round [144] log likelihood: -5243.634873
EM: Round [145] log likelihood: -5243.633773
EM: Round [146] log likelihood: -5243.632688
EM: Round [147] log likelihood: -5243.631619
EM: Round [148] log likelihood: -5243.630564
EM: Round [149] log likelihood: -5243.629523
EM: Round [150] log likelihood: -5243.628497
EM: Round [151] log likelihood: -5243.627485
EM: Round [152] log likelihood: -5243.626487
EM: Round [153] log likelihood: -5243.625502
EM: Round [154] log likelihood: -5243.624531
EM: Round [155] log likelihood: -5243.623573
EM: Round [156] log likelihood: -5243.622629
EM: Round [157] log likelihood: -5243.621697
EM: Round [158] log likelihood: -5243.620777
EM: Round [159] log likelihood: -5243.619870
EM: Round [160] log likelihood: -5243.618976
EM: Round [161] log likelihood: -5243.618093
EM: Round [162] log likelihood: -5243.617223
EM: Round [163] log likelihood: -5243.616364
EM: Round [164] log likelihood: -5243.615516
EM: Round [165] log likelihood: -5243.614680
EM: Round [166] log likelihood: -5243.613856
EM: Round [167] log likelihood: -5243.613042
EM: Round [168] log likelihood: -5243.612239
EM: Round [169] log likelihood: -5243.611447
EM: Round [170] log likelihood: -5243.610666
EM: Round [171] log likelihood: -5243.609895
EM: Round [172] log likelihood: -5243.609134
EM: Round [173] log likelihood: -5243.608383
EM: Round [174] log likelihood: -5243.607642
EM: Round [175] log likelihood: -5243.606912
EM: Round [176] log likelihood: -5243.606191
EM: Round [177] log likelihood: -5243.605479
EM: Round [178] log likelihood: -5243.604777
EM: Round [179] log likelihood: -5243.604084
EM: Round [180] log likelihood: -5243.603400
EM: Round [181] log likelihood: -5243.602726
EM: Round [182] log likelihood: -5243.602060
EM: Round [183] log likelihood: -5243.601403
EM: Round [184] log likelihood: -5243.600755
EM: Round [185] log likelihood: -5243.600115
EM: Round [186] log likelihood: -5243.599484
EM: Round [187] log likelihood: -5243.598860
EM: Round [188] log likelihood: -5243.598246
EM: Round [189] log likelihood: -5243.597639
EM: Round [190] log likelihood: -5243.597040
EM: Round [191] log likelihood: -5243.596449
EM: Round [192] log likelihood: -5243.595866
EM: Round [193] log likelihood: -5243.595290
EM: Round [194] log likelihood: -5243.594722
EM: Round [195] log likelihood: -5243.594162
EM: Round [196] log likelihood: -5243.593608
EM: Round [197] log likelihood: -5243.593062
EM: Round [198] log likelihood: -5243.592523
EM: Round [199] log likelihood: -5243.591991
EM: Round [200] log likelihood: -5243.591466
EM: Round [201] log likelihood: -5243.590948
EM: Round [202] log likelihood: -5243.590437
EM: Round [203] log likelihood: -5243.589932
EM: Round [204] log likelihood: -5243.589434
EM: Round [205] log likelihood: -5243.588942
EM: Round [206] log likelihood: -5243.588457
EM: Round [207] log likelihood: -5243.587978
EM: Round [208] log likelihood: -5243.587505
EM: Round [209] log likelihood: -5243.587039
EM: Round [210] log likelihood: -5243.586578
EM: Round [211] log likelihood: -5243.586123
EM: Round [212] log likelihood: -5243.585675
EM: Round [213] log likelihood: -5243.585232
EM: Round [214] log likelihood: -5243.584795
EM: Round [215] log likelihood: -5243.584363
EM: Round [216] log likelihood: -5243.583937
EM: Round [217] log likelihood: -5243.583517
EM: Round [218] log likelihood: -5243.583102
EM: Round [219] log likelihood: -5243.582692
EM: Round [220] log likelihood: -5243.582288
EM: Round [221] log likelihood: -5243.581889
EM: Round [222] log likelihood: -5243.581495
EM: Round [223] log likelihood: -5243.581106
EM: Round [224] log likelihood: -5243.580722
EM: Round [225] log likelihood: -5243.580343
EM: Round [226] log likelihood: -5243.579969
EM: Round [227] log likelihood: -5243.579599
EM: Round [228] log likelihood: -5243.579235
EM: Round [229] log likelihood: -5243.578875
EM: Round [230] log likelihood: -5243.578520
EM: Round [231] log likelihood: -5243.578169
EM: Round [232] log likelihood: -5243.577823
EM: Round [233] log likelihood: -5243.577481
EM: Round [234] log likelihood: -5243.577144
EM: Round [235] log likelihood: -5243.576811
EM: Round [236] log likelihood: -5243.576482
EM: Round [237] log likelihood: -5243.576158
EM: Round [238] log likelihood: -5243.575838
EM: Round [239] log likelihood: -5243.575521
EM: Round [240] log likelihood: -5243.575209
EM: Round [241] log likelihood: -5243.574901
EM: Round [242] log likelihood: -5243.574597
EM: Round [243] log likelihood: -5243.574297
EM: Round [244] log likelihood: -5243.574000
EM: Round [245] log likelihood: -5243.573707
EM: Round [246] log likelihood: -5243.573418
EM: Round [247] log likelihood: -5243.573133
EM: Round [248] log likelihood: -5243.572852
EM: Round [249] log likelihood: -5243.572574
EM: Round [250] log likelihood: -5243.572299
EM: Round [251] log likelihood: -5243.572028
EM: Round [252] log likelihood: -5243.571761
EM: Round [253] log likelihood: -5243.571497
EM: Round [254] log likelihood: -5243.571236
EM: Round [255] log likelihood: -5243.570979
EM: Round [256] log likelihood: -5243.570724
EM: Round [257] log likelihood: -5243.570474
EM: Round [258] log likelihood: -5243.570226
EM: Round [259] log likelihood: -5243.569981
EM: Round [260] log likelihood: -5243.569740
EM: Round [261] log likelihood: -5243.569502
EM: Round [262] log likelihood: -5243.569267
EM: Round [263] log likelihood: -5243.569034
EM: Round [264] log likelihood: -5243.568805
EM: Round [265] log likelihood: -5243.568578
EM: Round [266] log likelihood: -5243.568355
EM: Round [267] log likelihood: -5243.568134
EM: Round [268] log likelihood: -5243.567916
EM: Round [269] log likelihood: -5243.567701
EM: Round [270] log likelihood: -5243.567489
EM: Round [271] log likelihood: -5243.567279
EM: Round [272] log likelihood: -5243.567072
EM: Round [273] log likelihood: -5243.566868
EM: Round [274] log likelihood: -5243.566666
EM: Round [275] log likelihood: -5243.566467
EM: Round [276] log likelihood: -5243.566270
EM: Round [277] log likelihood: -5243.566076
EM: Round [278] log likelihood: -5243.565884
EM: Round [279] log likelihood: -5243.565695
EM: Round [280] log likelihood: -5243.565508
EM: Round [281] log likelihood: -5243.565324
EM: Round [282] log likelihood: -5243.565141
EM: Round [283] log likelihood: -5243.564962
EM: Round [284] log likelihood: -5243.564784
EM: Round [285] log likelihood: -5243.564609
EM: Round [286] log likelihood: -5243.564435
EM: Round [287] log likelihood: -5243.564265
EM: Round [288] log likelihood: -5243.564096
EM: Round [289] log likelihood: -5243.563929
EM: Round [290] log likelihood: -5243.563765
EM: Round [291] log likelihood: -5243.563602
EM: Round [292] log likelihood: -5243.563442
EM: Round [293] log likelihood: -5243.563283
EM: Round [294] log likelihood: -5243.563127
EM: Round [295] log likelihood: -5243.562973
EM: Round [296] log likelihood: -5243.562820
EM: Round [297] log likelihood: -5243.562670
EM: Round [298] log likelihood: -5243.562521
EM: Round [299] log likelihood: -5243.562375
EM: Round [300] log likelihood: -5243.562230
EM: Round [301] log likelihood: -5243.562087
EM: Round [302] log likelihood: -5243.561946
EM: Round [303] log likelihood: -5243.561806
EM: Round [304] log likelihood: -5243.561668
EM: Round [305] log likelihood: -5243.561533
EM: Round [306] log likelihood: -5243.561398
EM: Round [307] log likelihood: -5243.561266
EM: Round [308] log likelihood: -5243.561135
EM: Round [309] log likelihood: -5243.561006
EM: Round [310] log likelihood: -5243.560878
EM: Round [311] log likelihood: -5243.560752
EM: Round [312] log likelihood: -5243.560628
EM: Round [313] log likelihood: -5243.560505
EM: Round [314] log likelihood: -5243.560384
EM: Round [315] log likelihood: -5243.560264
EM: Round [316] log likelihood: -5243.560146
EM: Round [317] log likelihood: -5243.560029
EM: Round [318] log likelihood: -5243.559914
EM: Round [319] log likelihood: -5243.559800
EM: Round [320] log likelihood: -5243.559688
EM: Round [321] log likelihood: -5243.559577
EM: Round [322] log likelihood: -5243.559468
EM: Round [323] log likelihood: -5243.559359
EM: Round [324] log likelihood: -5243.559253
EM: Round [325] log likelihood: -5243.559147
EM: Round [326] log likelihood: -5243.559043
EM: Round [327] log likelihood: -5243.558940
EM: Round [328] log likelihood: -5243.558839
EM: Round [329] log likelihood: -5243.558739
EM: Round [330] log likelihood: -5243.558640
EM: Stopping iterations at round 330 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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/tih_rna_sample_00758_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa > /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/tih_rna_sample_00758_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir
-done, see /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3449.671044
EM: Round [1] log likelihood: -3449.668660
EM: Round [2] log likelihood: -3449.668628
EM: Stopping iterations at round 2 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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_1.fastp.fastq.gz: 295922654
Execution Time = 5.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa --gtf /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf  > /tmp/nxf.9BllnXalgH/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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fa --gtf /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.gtf  > /tmp/nxf.9BllnXalgH/fi_workdir/microH.dat
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.9BllnXalgH/fi_workdir/microH.dat /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_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.9BllnXalgH/fi_workdir/microH.dat /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.9BllnXalgH --json_outfile /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00758_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.9BllnXalgH --json_outfile /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00758_B23MVV7LT4_1
Running: touch /tmp/nxf.9BllnXalgH/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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00758_B23MVV7LT4_1 --html_output /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.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.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00758_B23MVV7LT4_1 --html_output /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
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 [ENSG00000259345.7]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.9BllnXalgH/ctat_genome_lib_build_dir > /tmp/nxf.9BllnXalgH/tih_rna_sample_00758_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.9BllnXalgH/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory