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/31/b9c0404e2960a48728db7c1b06ea00/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/b9c0404e2960a48728db7c1b06ea00/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/492d969cf2e534f41f20451df9699f/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/7792d5baa09478b2edbcc355ee8e22/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/492d969cf2e534f41f20451df9699f/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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 659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/cytoBand.txt
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.HEmYH06Pph/fi_workdir --reads "/tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:41:01 ..... started STAR run
Jun 08 10:41:01 ..... loading genome
Jun 08 10:42:45 ... generating Suffix Array index
Jun 08 10:46:41 ... completed Suffix Array index
Jun 08 10:46:41 ..... processing annotations GTF
Jun 08 10:46:42 ..... inserting junctions into the genome indices
Jun 08 10:47:45 ..... started mapping
Jun 08 12:29:07 ..... finished mapping
Jun 08 12:29:09 ..... started sorting BAM
Jun 08 12:29:10 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 108.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.HEmYH06Pph/fi_workdir --reads "/tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
12:29:32 : INFO : Done.
Execution Time = 0.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[3390000]   -done parsing /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 115,
          'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
          'per_id < 96' => 11798,
          'seq-similar region overlap' => 1606,
          'num genes matched < 2' => 57,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'small anchor length' => 243,
          ' ** passed ** ' => 42912,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 111,
          'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 505,
          'excessive soft clipping' => 20078,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 68,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 48,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 102,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 40,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 30,
          'low complexity anchor region' => 26
        };
-writing fusion junction support info.
Execution Time = 1.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[6000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[44000]   -fusion SPANNING read extraction for scaff: AC079781.4--ASNS

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[22000]   -fusion SPANNING read extraction for scaff: AC091132.4--AC091132.1

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[21000]   -fusion SPANNING read extraction for scaff: AC097532.3--GPR39

[1000]   -fusion SPANNING read extraction for scaff: AC138035.1--SEPTIN14

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[31000]   -fusion SPANNING read extraction for scaff: ADAMTS17--SPATA41

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[31000]   -fusion SPANNING read extraction for scaff: ADAMTS17--CERS3-AS1

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[9000]   -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180

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[565000]   -fusion SPANNING read extraction for scaff: EWSR1--FLI1

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[87000]   -fusion SPANNING read extraction for scaff: GUSB--NAIPP4

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

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[106000]   -fusion SPANNING read extraction for scaff: MCM3AP--MTRNR2L12

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[190000]   
[191000]   
[192000]   -fusion SPANNING read extraction for scaff: NKX2-2--NOC4L

[1000]   
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[6000]   
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[8000]   
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[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[20000]   
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[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[60000]   
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[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[14000]   
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[20000]   
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[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[20000]   
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[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[20000]   
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[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[20000]   
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[50000]   
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[60000]   
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[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]   
[87000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[13000]   
[14000]   
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[20000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
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[20000]   
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[70000]   
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[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
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[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: PCDHGA1--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8

[1000]   
[2000]   
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[4000]   
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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4

[1000]   
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[3000]   
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[6000]   
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[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
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[6000]   
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[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10

[1000]   
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[8000]   
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[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[87000]   
[88000]   
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[90000]   
[91000]   
[92000]   
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[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[25000]   
[26000]   
[27000]   
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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[46000]   
[47000]   
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[49000]   
[50000]   
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[60000]   
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[62000]   
[63000]   
[64000]   
[65000]   
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[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: PCDHGB3--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[12000]   
[13000]   
[14000]   
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[20000]   
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[30000]   
[31000]   
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[33000]   
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[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
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[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
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[23000]   
[24000]   
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[30000]   
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[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
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[46000]   
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[48000]   
[49000]   
[50000]   
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[79000]   
[80000]   
[81000]   
[82000]   
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[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[20000]   
[21000]   
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[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: SDHAP1--SMBD1P

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[18000]   
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[20000]   
[21000]   
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[25000]   
[26000]   
[27000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
[10000]   
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[12000]   
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[14000]   
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[20000]   
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[25000]   
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[27000]   
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[31000]   
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[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   -fusion SPANNING read extraction for scaff: TAS2R14--PRR4

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[20000]   
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[25000]   
[26000]   
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[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[13000]   
[14000]   
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[20000]   
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[27000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

[1000]   
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[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[6000]   
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[8000]   
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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: TMED7--TICAM2

[1000]   
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[6000]   
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[8000]   
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[20000]   
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[25000]   
[26000]   
[27000]   
[28000]   
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[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: TMEM244--ARHGAP18

[1000]   
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[44000]   -fusion SPANNING read extraction for scaff: TRIM59--IFT80

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[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[12000]   -fusion SPANNING read extraction for scaff: UBE2Q2P2--GOLGA6L10
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 234322,
          'lacks exon overlap' => 28530
        };
Execution Time = 4.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -22686.086059
EM: Round [1] log likelihood: -22641.631506
EM: Round [2] log likelihood: -22633.143414
EM: Round [3] log likelihood: -22626.490431
EM: Round [4] log likelihood: -22621.165259
EM: Round [5] log likelihood: -22616.865958
EM: Round [6] log likelihood: -22613.366415
EM: Round [7] log likelihood: -22610.494775
EM: Round [8] log likelihood: -22608.119160
EM: Round [9] log likelihood: -22606.137742
EM: Round [10] log likelihood: -22604.471645
EM: Round [11] log likelihood: -22603.059691
EM: Round [12] log likelihood: -22601.854381
EM: Round [13] log likelihood: -22600.818726
EM: Round [14] log likelihood: -22599.923747
EM: Round [15] log likelihood: -22599.146517
EM: Round [16] log likelihood: -22598.468681
EM: Round [17] log likelihood: -22597.875339
EM: Round [18] log likelihood: -22597.354243
EM: Round [19] log likelihood: -22596.895208
EM: Round [20] log likelihood: -22596.489680
EM: Round [21] log likelihood: -22596.130423
EM: Round [22] log likelihood: -22595.811276
EM: Round [23] log likelihood: -22595.526972
EM: Round [24] log likelihood: -22595.272991
EM: Round [25] log likelihood: -22595.045439
EM: Round [26] log likelihood: -22594.840959
EM: Round [27] log likelihood: -22594.656648
EM: Round [28] log likelihood: -22594.489992
EM: Round [29] log likelihood: -22594.338810
EM: Round [30] log likelihood: -22594.201207
EM: Round [31] log likelihood: -22594.075537
EM: Round [32] log likelihood: -22593.960365
EM: Round [33] log likelihood: -22593.854441
EM: Round [34] log likelihood: -22593.756674
EM: Round [35] log likelihood: -22593.666111
EM: Round [36] log likelihood: -22593.581919
EM: Round [37] log likelihood: -22593.503370
EM: Round [38] log likelihood: -22593.429825
EM: Round [39] log likelihood: -22593.360725
EM: Round [40] log likelihood: -22593.295578
EM: Round [41] log likelihood: -22593.233956
EM: Round [42] log likelihood: -22593.175478
EM: Round [43] log likelihood: -22593.119813
EM: Round [44] log likelihood: -22593.066667
EM: Round [45] log likelihood: -22593.015783
EM: Round [46] log likelihood: -22592.966935
EM: Round [47] log likelihood: -22592.919921
EM: Round [48] log likelihood: -22592.874566
EM: Round [49] log likelihood: -22592.830713
EM: Round [50] log likelihood: -22592.788225
EM: Round [51] log likelihood: -22592.746980
EM: Round [52] log likelihood: -22592.706869
EM: Round [53] log likelihood: -22592.667798
EM: Round [54] log likelihood: -22592.629682
EM: Round [55] log likelihood: -22592.592445
EM: Round [56] log likelihood: -22592.556021
EM: Round [57] log likelihood: -22592.520350
EM: Round [58] log likelihood: -22592.485380
EM: Round [59] log likelihood: -22592.451063
EM: Round [60] log likelihood: -22592.417358
EM: Round [61] log likelihood: -22592.384227
EM: Round [62] log likelihood: -22592.351636
EM: Round [63] log likelihood: -22592.319555
EM: Round [64] log likelihood: -22592.287957
EM: Round [65] log likelihood: -22592.256818
EM: Round [66] log likelihood: -22592.226117
EM: Round [67] log likelihood: -22592.195832
EM: Round [68] log likelihood: -22592.165947
EM: Round [69] log likelihood: -22592.136445
EM: Round [70] log likelihood: -22592.107312
EM: Round [71] log likelihood: -22592.078535
EM: Round [72] log likelihood: -22592.050100
EM: Round [73] log likelihood: -22592.021997
EM: Round [74] log likelihood: -22591.994216
EM: Round [75] log likelihood: -22591.966748
EM: Round [76] log likelihood: -22591.939583
EM: Round [77] log likelihood: -22591.912713
EM: Round [78] log likelihood: -22591.886133
EM: Round [79] log likelihood: -22591.859833
EM: Round [80] log likelihood: -22591.833809
EM: Round [81] log likelihood: -22591.808054
EM: Round [82] log likelihood: -22591.782562
EM: Round [83] log likelihood: -22591.757328
EM: Round [84] log likelihood: -22591.732347
EM: Round [85] log likelihood: -22591.707615
EM: Round [86] log likelihood: -22591.683127
EM: Round [87] log likelihood: -22591.658878
EM: Round [88] log likelihood: -22591.634865
EM: Round [89] log likelihood: -22591.611084
EM: Round [90] log likelihood: -22591.587531
EM: Round [91] log likelihood: -22591.564203
EM: Round [92] log likelihood: -22591.541096
EM: Round [93] log likelihood: -22591.518207
EM: Round [94] log likelihood: -22591.495533
EM: Round [95] log likelihood: -22591.473071
EM: Round [96] log likelihood: -22591.450817
EM: Round [97] log likelihood: -22591.428770
EM: Round [98] log likelihood: -22591.406925
EM: Round [99] log likelihood: -22591.385281
EM: Round [100] log likelihood: -22591.363835
EM: Round [101] log likelihood: -22591.342585
EM: Round [102] log likelihood: -22591.321527
EM: Round [103] log likelihood: -22591.300660
EM: Round [104] log likelihood: -22591.279981
EM: Round [105] log likelihood: -22591.259487
EM: Round [106] log likelihood: -22591.239177
EM: Round [107] log likelihood: -22591.219049
EM: Round [108] log likelihood: -22591.199099
EM: Round [109] log likelihood: -22591.179327
EM: Round [110] log likelihood: -22591.159729
EM: Round [111] log likelihood: -22591.140305
EM: Round [112] log likelihood: -22591.121051
EM: Round [113] log likelihood: -22591.101966
EM: Round [114] log likelihood: -22591.083049
EM: Round [115] log likelihood: -22591.064296
EM: Round [116] log likelihood: -22591.045706
EM: Round [117] log likelihood: -22591.027278
EM: Round [118] log likelihood: -22591.009010
EM: Round [119] log likelihood: -22590.990899
EM: Round [120] log likelihood: -22590.972945
EM: Round [121] log likelihood: -22590.955145
EM: Round [122] log likelihood: -22590.937497
EM: Round [123] log likelihood: -22590.920001
EM: Round [124] log likelihood: -22590.902653
EM: Round [125] log likelihood: -22590.885454
EM: Round [126] log likelihood: -22590.868401
EM: Round [127] log likelihood: -22590.851492
EM: Round [128] log likelihood: -22590.834727
EM: Round [129] log likelihood: -22590.818102
EM: Round [130] log likelihood: -22590.801619
EM: Round [131] log likelihood: -22590.785273
EM: Round [132] log likelihood: -22590.769065
EM: Round [133] log likelihood: -22590.752992
EM: Round [134] log likelihood: -22590.737054
EM: Round [135] log likelihood: -22590.721248
EM: Round [136] log likelihood: -22590.705574
EM: Round [137] log likelihood: -22590.690030
EM: Round [138] log likelihood: -22590.674615
EM: Round [139] log likelihood: -22590.659328
EM: Round [140] log likelihood: -22590.644166
EM: Round [141] log likelihood: -22590.629130
EM: Round [142] log likelihood: -22590.614217
EM: Round [143] log likelihood: -22590.599427
EM: Round [144] log likelihood: -22590.584757
EM: Round [145] log likelihood: -22590.570208
EM: Round [146] log likelihood: -22590.555777
EM: Round [147] log likelihood: -22590.541464
EM: Round [148] log likelihood: -22590.527268
EM: Round [149] log likelihood: -22590.513186
EM: Round [150] log likelihood: -22590.499219
EM: Round [151] log likelihood: -22590.485364
EM: Round [152] log likelihood: -22590.471622
EM: Round [153] log likelihood: -22590.457990
EM: Round [154] log likelihood: -22590.444468
EM: Round [155] log likelihood: -22590.431054
EM: Round [156] log likelihood: -22590.417748
EM: Round [157] log likelihood: -22590.404549
EM: Round [158] log likelihood: -22590.391455
EM: Round [159] log likelihood: -22590.378465
EM: Round [160] log likelihood: -22590.365579
EM: Round [161] log likelihood: -22590.352795
EM: Round [162] log likelihood: -22590.340113
EM: Round [163] log likelihood: -22590.327531
EM: Round [164] log likelihood: -22590.315049
EM: Round [165] log likelihood: -22590.302666
EM: Round [166] log likelihood: -22590.290380
EM: Round [167] log likelihood: -22590.278191
EM: Round [168] log likelihood: -22590.266098
EM: Round [169] log likelihood: -22590.254099
EM: Round [170] log likelihood: -22590.242195
EM: Round [171] log likelihood: -22590.230384
EM: Round [172] log likelihood: -22590.218666
EM: Round [173] log likelihood: -22590.207038
EM: Round [174] log likelihood: -22590.195502
EM: Round [175] log likelihood: -22590.184055
EM: Round [176] log likelihood: -22590.172697
EM: Round [177] log likelihood: -22590.161427
EM: Round [178] log likelihood: -22590.150245
EM: Round [179] log likelihood: -22590.139149
EM: Round [180] log likelihood: -22590.128138
EM: Round [181] log likelihood: -22590.117213
EM: Round [182] log likelihood: -22590.106372
EM: Round [183] log likelihood: -22590.095614
EM: Round [184] log likelihood: -22590.084939
EM: Round [185] log likelihood: -22590.074346
EM: Round [186] log likelihood: -22590.063834
EM: Round [187] log likelihood: -22590.053402
EM: Round [188] log likelihood: -22590.043050
EM: Round [189] log likelihood: -22590.032777
EM: Round [190] log likelihood: -22590.022582
EM: Round [191] log likelihood: -22590.012465
EM: Round [192] log likelihood: -22590.002425
EM: Round [193] log likelihood: -22589.992461
EM: Round [194] log likelihood: -22589.982573
EM: Round [195] log likelihood: -22589.972759
EM: Round [196] log likelihood: -22589.963020
EM: Round [197] log likelihood: -22589.953354
EM: Round [198] log likelihood: -22589.943761
EM: Round [199] log likelihood: -22589.934240
EM: Round [200] log likelihood: -22589.924791
EM: Round [201] log likelihood: -22589.915413
EM: Round [202] log likelihood: -22589.906106
EM: Round [203] log likelihood: -22589.896868
EM: Round [204] log likelihood: -22589.887699
EM: Round [205] log likelihood: -22589.878599
EM: Round [206] log likelihood: -22589.869567
EM: Round [207] log likelihood: -22589.860602
EM: Round [208] log likelihood: -22589.851704
EM: Round [209] log likelihood: -22589.842873
EM: Round [210] log likelihood: -22589.834107
EM: Round [211] log likelihood: -22589.825406
EM: Round [212] log likelihood: -22589.816769
EM: Round [213] log likelihood: -22589.808197
EM: Round [214] log likelihood: -22589.799688
EM: Round [215] log likelihood: -22589.791242
EM: Round [216] log likelihood: -22589.782858
EM: Round [217] log likelihood: -22589.774537
EM: Round [218] log likelihood: -22589.766276
EM: Round [219] log likelihood: -22589.758076
EM: Round [220] log likelihood: -22589.749937
EM: Round [221] log likelihood: -22589.741857
EM: Round [222] log likelihood: -22589.733837
EM: Round [223] log likelihood: -22589.725875
EM: Round [224] log likelihood: -22589.717972
EM: Round [225] log likelihood: -22589.710126
EM: Round [226] log likelihood: -22589.702338
EM: Round [227] log likelihood: -22589.694607
EM: Round [228] log likelihood: -22589.686932
EM: Round [229] log likelihood: -22589.679313
EM: Round [230] log likelihood: -22589.671749
EM: Round [231] log likelihood: -22589.664240
EM: Round [232] log likelihood: -22589.656786
EM: Round [233] log likelihood: -22589.649386
EM: Round [234] log likelihood: -22589.642039
EM: Round [235] log likelihood: -22589.634746
EM: Round [236] log likelihood: -22589.627506
EM: Round [237] log likelihood: -22589.620317
EM: Round [238] log likelihood: -22589.613181
EM: Round [239] log likelihood: -22589.606096
EM: Round [240] log likelihood: -22589.599062
EM: Round [241] log likelihood: -22589.592079
EM: Round [242] log likelihood: -22589.585146
EM: Round [243] log likelihood: -22589.578262
EM: Round [244] log likelihood: -22589.571429
EM: Round [245] log likelihood: -22589.564644
EM: Round [246] log likelihood: -22589.557907
EM: Round [247] log likelihood: -22589.551219
EM: Round [248] log likelihood: -22589.544579
EM: Round [249] log likelihood: -22589.537986
EM: Round [250] log likelihood: -22589.531441
EM: Round [251] log likelihood: -22589.524941
EM: Round [252] log likelihood: -22589.518489
EM: Round [253] log likelihood: -22589.512082
EM: Round [254] log likelihood: -22589.505720
EM: Round [255] log likelihood: -22589.499404
EM: Round [256] log likelihood: -22589.493133
EM: Round [257] log likelihood: -22589.486906
EM: Round [258] log likelihood: -22589.480724
EM: Round [259] log likelihood: -22589.474585
EM: Round [260] log likelihood: -22589.468489
EM: Round [261] log likelihood: -22589.462437
EM: Round [262] log likelihood: -22589.456427
EM: Round [263] log likelihood: -22589.450460
EM: Round [264] log likelihood: -22589.444535
EM: Round [265] log likelihood: -22589.438651
EM: Round [266] log likelihood: -22589.432809
EM: Round [267] log likelihood: -22589.427008
EM: Round [268] log likelihood: -22589.421248
EM: Round [269] log likelihood: -22589.415528
EM: Round [270] log likelihood: -22589.409848
EM: Round [271] log likelihood: -22589.404209
EM: Round [272] log likelihood: -22589.398608
EM: Round [273] log likelihood: -22589.393047
EM: Round [274] log likelihood: -22589.387525
EM: Round [275] log likelihood: -22589.382041
EM: Round [276] log likelihood: -22589.376596
EM: Round [277] log likelihood: -22589.371188
EM: Round [278] log likelihood: -22589.365818
EM: Round [279] log likelihood: -22589.360486
EM: Round [280] log likelihood: -22589.355191
EM: Round [281] log likelihood: -22589.349932
EM: Round [282] log likelihood: -22589.344710
EM: Round [283] log likelihood: -22589.339525
EM: Round [284] log likelihood: -22589.334375
EM: Round [285] log likelihood: -22589.329261
EM: Round [286] log likelihood: -22589.324182
EM: Round [287] log likelihood: -22589.319139
EM: Round [288] log likelihood: -22589.314130
EM: Round [289] log likelihood: -22589.309157
EM: Round [290] log likelihood: -22589.304217
EM: Round [291] log likelihood: -22589.299312
EM: Round [292] log likelihood: -22589.294440
EM: Round [293] log likelihood: -22589.289602
EM: Round [294] log likelihood: -22589.284797
EM: Round [295] log likelihood: -22589.280025
EM: Round [296] log likelihood: -22589.275286
EM: Round [297] log likelihood: -22589.270580
EM: Round [298] log likelihood: -22589.265906
EM: Round [299] log likelihood: -22589.261264
EM: Round [300] log likelihood: -22589.256654
EM: Round [301] log likelihood: -22589.252075
EM: Round [302] log likelihood: -22589.247528
EM: Round [303] log likelihood: -22589.243012
EM: Round [304] log likelihood: -22589.238527
EM: Round [305] log likelihood: -22589.234072
EM: Round [306] log likelihood: -22589.229648
EM: Round [307] log likelihood: -22589.225254
EM: Round [308] log likelihood: -22589.220890
EM: Round [309] log likelihood: -22589.216556
EM: Round [310] log likelihood: -22589.212251
EM: Round [311] log likelihood: -22589.207976
EM: Round [312] log likelihood: -22589.203729
EM: Round [313] log likelihood: -22589.199512
EM: Round [314] log likelihood: -22589.195323
EM: Round [315] log likelihood: -22589.191162
EM: Round [316] log likelihood: -22589.187030
EM: Round [317] log likelihood: -22589.182926
EM: Round [318] log likelihood: -22589.178849
EM: Round [319] log likelihood: -22589.174800
EM: Round [320] log likelihood: -22589.170779
EM: Round [321] log likelihood: -22589.166785
EM: Round [322] log likelihood: -22589.162817
EM: Round [323] log likelihood: -22589.158877
EM: Round [324] log likelihood: -22589.154963
EM: Round [325] log likelihood: -22589.151075
EM: Round [326] log likelihood: -22589.147214
EM: Round [327] log likelihood: -22589.143378
EM: Round [328] log likelihood: -22589.139569
EM: Round [329] log likelihood: -22589.135785
EM: Round [330] log likelihood: -22589.132026
EM: Round [331] log likelihood: -22589.128293
EM: Round [332] log likelihood: -22589.124585
EM: Round [333] log likelihood: -22589.120901
EM: Round [334] log likelihood: -22589.117243
EM: Round [335] log likelihood: -22589.113609
EM: Round [336] log likelihood: -22589.109999
EM: Round [337] log likelihood: -22589.106413
EM: Round [338] log likelihood: -22589.102851
EM: Round [339] log likelihood: -22589.099313
EM: Round [340] log likelihood: -22589.095799
EM: Round [341] log likelihood: -22589.092308
EM: Round [342] log likelihood: -22589.088841
EM: Round [343] log likelihood: -22589.085397
EM: Round [344] log likelihood: -22589.081975
EM: Round [345] log likelihood: -22589.078576
EM: Round [346] log likelihood: -22589.075200
EM: Round [347] log likelihood: -22589.071847
EM: Round [348] log likelihood: -22589.068516
EM: Round [349] log likelihood: -22589.065206
EM: Round [350] log likelihood: -22589.061919
EM: Round [351] log likelihood: -22589.058654
EM: Round [352] log likelihood: -22589.055410
EM: Round [353] log likelihood: -22589.052188
EM: Round [354] log likelihood: -22589.048987
EM: Round [355] log likelihood: -22589.045808
EM: Round [356] log likelihood: -22589.042649
EM: Round [357] log likelihood: -22589.039511
EM: Round [358] log likelihood: -22589.036394
EM: Round [359] log likelihood: -22589.033298
EM: Round [360] log likelihood: -22589.030222
EM: Round [361] log likelihood: -22589.027166
EM: Round [362] log likelihood: -22589.024131
EM: Round [363] log likelihood: -22589.021115
EM: Round [364] log likelihood: -22589.018120
EM: Round [365] log likelihood: -22589.015144
EM: Round [366] log likelihood: -22589.012187
EM: Round [367] log likelihood: -22589.009251
EM: Round [368] log likelihood: -22589.006333
EM: Round [369] log likelihood: -22589.003435
EM: Round [370] log likelihood: -22589.000555
EM: Round [371] log likelihood: -22588.997695
EM: Round [372] log likelihood: -22588.994853
EM: Round [373] log likelihood: -22588.992030
EM: Round [374] log likelihood: -22588.989225
EM: Round [375] log likelihood: -22588.986439
EM: Round [376] log likelihood: -22588.983671
EM: Round [377] log likelihood: -22588.980921
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EM: Round [834] log likelihood: -22588.566657
EM: Round [835] log likelihood: -22588.566474
EM: Round [836] log likelihood: -22588.566293
EM: Round [837] log likelihood: -22588.566113
EM: Round [838] log likelihood: -22588.565933
EM: Round [839] log likelihood: -22588.565755
EM: Round [840] log likelihood: -22588.565577
EM: Round [841] log likelihood: -22588.565401
EM: Round [842] log likelihood: -22588.565225
EM: Round [843] log likelihood: -22588.565050
EM: Round [844] log likelihood: -22588.564876
EM: Round [845] log likelihood: -22588.564703
EM: Round [846] log likelihood: -22588.564531
EM: Round [847] log likelihood: -22588.564360
EM: Round [848] log likelihood: -22588.564190
EM: Round [849] log likelihood: -22588.564021
EM: Round [850] log likelihood: -22588.563852
EM: Round [851] log likelihood: -22588.563685
EM: Round [852] log likelihood: -22588.563518
EM: Round [853] log likelihood: -22588.563352
EM: Round [854] log likelihood: -22588.563187
EM: Round [855] log likelihood: -22588.563023
EM: Round [856] log likelihood: -22588.562860
EM: Round [857] log likelihood: -22588.562698
EM: Round [858] log likelihood: -22588.562536
EM: Round [859] log likelihood: -22588.562375
EM: Round [860] log likelihood: -22588.562215
EM: Round [861] log likelihood: -22588.562056
EM: Round [862] log likelihood: -22588.561898
EM: Round [863] log likelihood: -22588.561741
EM: Round [864] log likelihood: -22588.561584
EM: Round [865] log likelihood: -22588.561428
EM: Round [866] log likelihood: -22588.561274
EM: Round [867] log likelihood: -22588.561119
EM: Round [868] log likelihood: -22588.560966
EM: Round [869] log likelihood: -22588.560813
EM: Round [870] log likelihood: -22588.560662
EM: Round [871] log likelihood: -22588.560511
EM: Round [872] log likelihood: -22588.560360
EM: Round [873] log likelihood: -22588.560211
EM: Round [874] log likelihood: -22588.560062
EM: Round [875] log likelihood: -22588.559914
EM: Round [876] log likelihood: -22588.559767
EM: Round [877] log likelihood: -22588.559621
EM: Round [878] log likelihood: -22588.559475
EM: Round [879] log likelihood: -22588.559330
EM: Round [880] log likelihood: -22588.559186
EM: Round [881] log likelihood: -22588.559043
EM: Round [882] log likelihood: -22588.558900
EM: Round [883] log likelihood: -22588.558758
EM: Round [884] log likelihood: -22588.558617
EM: Round [885] log likelihood: -22588.558477
EM: Round [886] log likelihood: -22588.558337
EM: Round [887] log likelihood: -22588.558198
EM: Round [888] log likelihood: -22588.558059
EM: Round [889] log likelihood: -22588.557922
EM: Round [890] log likelihood: -22588.557785
EM: Round [891] log likelihood: -22588.557648
EM: Round [892] log likelihood: -22588.557513
EM: Round [893] log likelihood: -22588.557378
EM: Round [894] log likelihood: -22588.557244
EM: Round [895] log likelihood: -22588.557110
EM: Round [896] log likelihood: -22588.556978
EM: Round [897] log likelihood: -22588.556845
EM: Round [898] log likelihood: -22588.556714
EM: Round [899] log likelihood: -22588.556583
EM: Round [900] log likelihood: -22588.556453
EM: Round [901] log likelihood: -22588.556323
EM: Round [902] log likelihood: -22588.556195
EM: Round [903] log likelihood: -22588.556066
EM: Round [904] log likelihood: -22588.555939
EM: Round [905] log likelihood: -22588.555812
EM: Round [906] log likelihood: -22588.555686
EM: Round [907] log likelihood: -22588.555560
EM: Round [908] log likelihood: -22588.555435
EM: Round [909] log likelihood: -22588.555311
EM: Round [910] log likelihood: -22588.555187
EM: Round [911] log likelihood: -22588.555064
EM: Round [912] log likelihood: -22588.554941
EM: Round [913] log likelihood: -22588.554819
EM: Round [914] log likelihood: -22588.554698
EM: Round [915] log likelihood: -22588.554578
EM: Round [916] log likelihood: -22588.554457
EM: Round [917] log likelihood: -22588.554338
EM: Round [918] log likelihood: -22588.554219
EM: Round [919] log likelihood: -22588.554101
EM: Round [920] log likelihood: -22588.553983
EM: Round [921] log likelihood: -22588.553866
EM: Round [922] log likelihood: -22588.553750
EM: Round [923] log likelihood: -22588.553634
EM: Round [924] log likelihood: -22588.553518
EM: Round [925] log likelihood: -22588.553403
EM: Round [926] log likelihood: -22588.553289
EM: Round [927] log likelihood: -22588.553176
EM: Round [928] log likelihood: -22588.553062
EM: Round [929] log likelihood: -22588.552950
EM: Round [930] log likelihood: -22588.552838
EM: Round [931] log likelihood: -22588.552727
EM: Round [932] log likelihood: -22588.552616
EM: Round [933] log likelihood: -22588.552505
EM: Round [934] log likelihood: -22588.552396
EM: Round [935] log likelihood: -22588.552286
EM: Round [936] log likelihood: -22588.552178
EM: Round [937] log likelihood: -22588.552070
EM: Round [938] log likelihood: -22588.551962
EM: Round [939] log likelihood: -22588.551855
EM: Round [940] log likelihood: -22588.551748
EM: Round [941] log likelihood: -22588.551642
EM: Round [942] log likelihood: -22588.551537
EM: Round [943] log likelihood: -22588.551432
EM: Round [944] log likelihood: -22588.551327
EM: Round [945] log likelihood: -22588.551223
EM: Round [946] log likelihood: -22588.551120
EM: Round [947] log likelihood: -22588.551017
EM: Round [948] log likelihood: -22588.550914
EM: Round [949] log likelihood: -22588.550812
EM: Round [950] log likelihood: -22588.550711
EM: Round [951] log likelihood: -22588.550610
EM: Round [952] log likelihood: -22588.550509
EM: Round [953] log likelihood: -22588.550409
EM: Stopping iterations at round 953 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.84 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir
-done, see /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -16195.754994
EM: Round [1] log likelihood: -16191.619086
EM: Round [2] log likelihood: -16191.592622
EM: Round [3] log likelihood: -16191.592107
EM: Round [4] log likelihood: -16191.592094
EM: Stopping iterations at round 4 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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295934893
Execution Time = 5.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.HEmYH06Pph/fi_workdir/microH.dat
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.HEmYH06Pph/fi_workdir/microH.dat /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_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.HEmYH06Pph/fi_workdir/microH.dat /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.HEmYH06Pph --json_outfile /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.HEmYH06Pph --json_outfile /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.HEmYH06Pph/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.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_eGK-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
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 [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000259429.5]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000251634.2]
WARNING, no entry stored in dbm for [ENSG00000286833.1]
WARNING, no entry stored in dbm for [ENSG00000286833.1]
WARNING, no entry stored in dbm for [ENSG00000261318.1]
WARNING, no entry stored in dbm for [ENSG00000261318.1]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000283426.1]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.HEmYH06Pph/ctat_genome_lib_build_dir > /tmp/nxf.HEmYH06Pph/659_eGK-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.HEmYH06Pph/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory