Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/8fed94442a4123416eec9b5b4b3712/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
  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/a6/e5c2c4eac291e3f209dd3e240c5319/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/e5c2c4eac291e3f209dd3e240c5319/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/acac48a28890fbbbac914665897a81/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/acac48a28890fbbbac914665897a81/659_bNS-T1-TRNA-1_B23MHV2LT4_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 659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.DnlGn3U1iD/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.DnlGn3U1iD/cytoBand.txt
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.DnlGn3U1iD/fi_workdir --reads "/tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 04 22:15:55 ..... started STAR run
Jun 04 22:15:55 ..... loading genome
Jun 04 22:18:29 ... generating Suffix Array index
Jun 04 22:24:36 ... completed Suffix Array index
Jun 04 22:24:37 ..... processing annotations GTF
Jun 04 22:24:37 ..... inserting junctions into the genome indices
Jun 04 22:26:05 ..... started mapping
Jun 04 23:25:14 ..... finished mapping
Jun 04 23:25:16 ..... started sorting BAM
Jun 04 23:25:17 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 69.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.DnlGn3U1iD/fi_workdir --reads "/tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
23:25:26 : INFO : Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[1340000]   -done parsing /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 202,
          'per_id < 96' => 4234,
          ' ** passed ** ' => 24892,
          'num genes matched < 2' => 4,
          'excessive soft clipping' => 5701,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2,
          'low complexity anchor region' => 1,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
          'small anchor length' => 251,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 36,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
          'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 2,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 29
        };
-writing fusion junction support info.
Execution Time = 0.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[25000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[156000]   
[157000]   
[158000]   
[159000]   
[160000]   
[161000]   
[162000]   
[163000]   
[164000]   
[165000]   
[166000]   
[167000]   
[168000]   
[169000]   
[170000]   
[171000]   
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[173000]   
[174000]   
[175000]   
[176000]   
[177000]   
[178000]   
[179000]   
[180000]   
[181000]   
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[183000]   
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[185000]   
[186000]   
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[189000]   
[190000]   
[191000]   
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[193000]   
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[198000]   
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[200000]   
[201000]   
[202000]   
[203000]   
[204000]   
[205000]   
[206000]   
[207000]   
[208000]   
[209000]   
[210000]   
[211000]   
[212000]   
[213000]   
[214000]   
[215000]   
[216000]   
[217000]   
[218000]   
[219000]   
[220000]   
[221000]   
[222000]   
[223000]   
[224000]   
[225000]   
[226000]   
[227000]   
[228000]   
[229000]   
[230000]   
[231000]   
[232000]   
[233000]   
[234000]   
[235000]   
[236000]   
[237000]   
[238000]   
[239000]   
[240000]   
[241000]   
[242000]   
[243000]   
[244000]   
[245000]   
[246000]   
[247000]   
[248000]   
[249000]   
[250000]   
[251000]   
[252000]   
[253000]   
[254000]   
[255000]   -fusion SPANNING read extraction for scaff: EML4--ALK

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: FBXO25--AL669831.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   -fusion SPANNING read extraction for scaff: IGFL1P2--HIF3A

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[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]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[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]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[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]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[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: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[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]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   -fusion SPANNING read extraction for scaff: PCDHGB2--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]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: SNTB2--TANGO6

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[36000]   -fusion SPANNING read extraction for scaff: TMEM120B--ORAI1

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[24000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 47107,
          'lacks exon overlap' => 2751
        };
Execution Time = 1.55 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6251.261430
EM: Round [1] log likelihood: -6249.295912
EM: Round [2] log likelihood: -6248.153621
EM: Round [3] log likelihood: -6247.348161
EM: Round [4] log likelihood: -6246.754854
EM: Round [5] log likelihood: -6246.296891
EM: Round [6] log likelihood: -6245.926315
EM: Round [7] log likelihood: -6245.612938
EM: Round [8] log likelihood: -6245.337664
EM: Round [9] log likelihood: -6245.088374
EM: Round [10] log likelihood: -6244.857362
EM: Round [11] log likelihood: -6244.639730
EM: Round [12] log likelihood: -6244.432360
EM: Round [13] log likelihood: -6244.233277
EM: Round [14] log likelihood: -6244.041227
EM: Round [15] log likelihood: -6243.855420
EM: Round [16] log likelihood: -6243.675355
EM: Round [17] log likelihood: -6243.500719
EM: Round [18] log likelihood: -6243.331306
EM: Round [19] log likelihood: -6243.166983
EM: Round [20] log likelihood: -6243.007653
EM: Round [21] log likelihood: -6242.853243
EM: Round [22] log likelihood: -6242.703685
EM: Round [23] log likelihood: -6242.558915
EM: Round [24] log likelihood: -6242.418867
EM: Round [25] log likelihood: -6242.283467
EM: Round [26] log likelihood: -6242.152639
EM: Round [27] log likelihood: -6242.026296
EM: Round [28] log likelihood: -6241.904347
EM: Round [29] log likelihood: -6241.786694
EM: Round [30] log likelihood: -6241.673234
EM: Round [31] log likelihood: -6241.563859
EM: Round [32] log likelihood: -6241.458459
EM: Round [33] log likelihood: -6241.356918
EM: Round [34] log likelihood: -6241.259120
EM: Round [35] log likelihood: -6241.164947
EM: Round [36] log likelihood: -6241.074281
EM: Round [37] log likelihood: -6240.987002
EM: Round [38] log likelihood: -6240.902993
EM: Round [39] log likelihood: -6240.822136
EM: Round [40] log likelihood: -6240.744316
EM: Round [41] log likelihood: -6240.669419
EM: Round [42] log likelihood: -6240.597332
EM: Round [43] log likelihood: -6240.527948
EM: Round [44] log likelihood: -6240.461158
EM: Round [45] log likelihood: -6240.396860
EM: Round [46] log likelihood: -6240.334953
EM: Round [47] log likelihood: -6240.275338
EM: Round [48] log likelihood: -6240.217921
EM: Round [49] log likelihood: -6240.162612
EM: Round [50] log likelihood: -6240.109321
EM: Round [51] log likelihood: -6240.057964
EM: Round [52] log likelihood: -6240.008459
EM: Round [53] log likelihood: -6239.960729
EM: Round [54] log likelihood: -6239.914696
EM: Round [55] log likelihood: -6239.870290
EM: Round [56] log likelihood: -6239.827441
EM: Round [57] log likelihood: -6239.786083
EM: Round [58] log likelihood: -6239.746151
EM: Round [59] log likelihood: -6239.707586
EM: Round [60] log likelihood: -6239.670329
EM: Round [61] log likelihood: -6239.634326
EM: Round [62] log likelihood: -6239.599522
EM: Round [63] log likelihood: -6239.565867
EM: Round [64] log likelihood: -6239.533313
EM: Round [65] log likelihood: -6239.501815
EM: Round [66] log likelihood: -6239.471327
EM: Round [67] log likelihood: -6239.441808
EM: Round [68] log likelihood: -6239.413219
EM: Round [69] log likelihood: -6239.385521
EM: Round [70] log likelihood: -6239.358677
EM: Round [71] log likelihood: -6239.332653
EM: Round [72] log likelihood: -6239.307417
EM: Round [73] log likelihood: -6239.282936
EM: Round [74] log likelihood: -6239.259181
EM: Round [75] log likelihood: -6239.236123
EM: Round [76] log likelihood: -6239.213734
EM: Round [77] log likelihood: -6239.191989
EM: Round [78] log likelihood: -6239.170862
EM: Round [79] log likelihood: -6239.150331
EM: Round [80] log likelihood: -6239.130373
EM: Round [81] log likelihood: -6239.110965
EM: Round [82] log likelihood: -6239.092088
EM: Round [83] log likelihood: -6239.073721
EM: Round [84] log likelihood: -6239.055846
EM: Round [85] log likelihood: -6239.038445
EM: Round [86] log likelihood: -6239.021501
EM: Round [87] log likelihood: -6239.004998
EM: Round [88] log likelihood: -6238.988919
EM: Round [89] log likelihood: -6238.973251
EM: Round [90] log likelihood: -6238.957978
EM: Round [91] log likelihood: -6238.943086
EM: Round [92] log likelihood: -6238.928564
EM: Round [93] log likelihood: -6238.914397
EM: Round [94] log likelihood: -6238.900575
EM: Round [95] log likelihood: -6238.887085
EM: Round [96] log likelihood: -6238.873917
EM: Round [97] log likelihood: -6238.861059
EM: Round [98] log likelihood: -6238.848503
EM: Round [99] log likelihood: -6238.836237
EM: Round [100] log likelihood: -6238.824254
EM: Round [101] log likelihood: -6238.812542
EM: Round [102] log likelihood: -6238.801095
EM: Round [103] log likelihood: -6238.789904
EM: Round [104] log likelihood: -6238.778960
EM: Round [105] log likelihood: -6238.768256
EM: Round [106] log likelihood: -6238.757785
EM: Round [107] log likelihood: -6238.747540
EM: Round [108] log likelihood: -6238.737514
EM: Round [109] log likelihood: -6238.727699
EM: Round [110] log likelihood: -6238.718091
EM: Round [111] log likelihood: -6238.708682
EM: Round [112] log likelihood: -6238.699467
EM: Round [113] log likelihood: -6238.690441
EM: Round [114] log likelihood: -6238.681597
EM: Round [115] log likelihood: -6238.672930
EM: Round [116] log likelihood: -6238.664436
EM: Round [117] log likelihood: -6238.656109
EM: Round [118] log likelihood: -6238.647945
EM: Round [119] log likelihood: -6238.639939
EM: Round [120] log likelihood: -6238.632087
EM: Round [121] log likelihood: -6238.624384
EM: Round [122] log likelihood: -6238.616827
EM: Round [123] log likelihood: -6238.609411
EM: Round [124] log likelihood: -6238.602132
EM: Round [125] log likelihood: -6238.594987
EM: Round [126] log likelihood: -6238.587971
EM: Round [127] log likelihood: -6238.581083
EM: Round [128] log likelihood: -6238.574317
EM: Round [129] log likelihood: -6238.567672
EM: Round [130] log likelihood: -6238.561143
EM: Round [131] log likelihood: -6238.554727
EM: Round [132] log likelihood: -6238.548422
EM: Round [133] log likelihood: -6238.542225
EM: Round [134] log likelihood: -6238.536133
EM: Round [135] log likelihood: -6238.530143
EM: Round [136] log likelihood: -6238.524252
EM: Round [137] log likelihood: -6238.518459
EM: Round [138] log likelihood: -6238.512760
EM: Round [139] log likelihood: -6238.507153
EM: Round [140] log likelihood: -6238.501636
EM: Round [141] log likelihood: -6238.496206
EM: Round [142] log likelihood: -6238.490862
EM: Round [143] log likelihood: -6238.485601
EM: Round [144] log likelihood: -6238.480420
EM: Round [145] log likelihood: -6238.475319
EM: Round [146] log likelihood: -6238.470296
EM: Round [147] log likelihood: -6238.465347
EM: Round [148] log likelihood: -6238.460471
EM: Round [149] log likelihood: -6238.455668
EM: Round [150] log likelihood: -6238.450934
EM: Round [151] log likelihood: -6238.446268
EM: Round [152] log likelihood: -6238.441669
EM: Round [153] log likelihood: -6238.437134
EM: Round [154] log likelihood: -6238.432663
EM: Round [155] log likelihood: -6238.428254
EM: Round [156] log likelihood: -6238.423905
EM: Round [157] log likelihood: -6238.419616
EM: Round [158] log likelihood: -6238.415383
EM: Round [159] log likelihood: -6238.411207
EM: Round [160] log likelihood: -6238.407086
EM: Round [161] log likelihood: -6238.403018
EM: Round [162] log likelihood: -6238.399003
EM: Round [163] log likelihood: -6238.395039
EM: Round [164] log likelihood: -6238.391125
EM: Round [165] log likelihood: -6238.387259
EM: Round [166] log likelihood: -6238.383441
EM: Round [167] log likelihood: -6238.379670
EM: Round [168] log likelihood: -6238.375945
EM: Round [169] log likelihood: -6238.372264
EM: Round [170] log likelihood: -6238.368626
EM: Round [171] log likelihood: -6238.365031
EM: Round [172] log likelihood: -6238.361478
EM: Round [173] log likelihood: -6238.357965
EM: Round [174] log likelihood: -6238.354492
EM: Round [175] log likelihood: -6238.351058
EM: Round [176] log likelihood: -6238.347662
EM: Round [177] log likelihood: -6238.344303
EM: Round [178] log likelihood: -6238.340981
EM: Round [179] log likelihood: -6238.337694
EM: Round [180] log likelihood: -6238.334442
EM: Round [181] log likelihood: -6238.331224
EM: Round [182] log likelihood: -6238.328040
EM: Round [183] log likelihood: -6238.324888
EM: Round [184] log likelihood: -6238.321768
EM: Round [185] log likelihood: -6238.318679
EM: Round [186] log likelihood: -6238.315621
EM: Round [187] log likelihood: -6238.312593
EM: Round [188] log likelihood: -6238.309594
EM: Round [189] log likelihood: -6238.306624
EM: Round [190] log likelihood: -6238.303682
EM: Round [191] log likelihood: -6238.300768
EM: Round [192] log likelihood: -6238.297880
EM: Round [193] log likelihood: -6238.295020
EM: Round [194] log likelihood: -6238.292185
EM: Round [195] log likelihood: -6238.289375
EM: Round [196] log likelihood: -6238.286590
EM: Round [197] log likelihood: -6238.283830
EM: Round [198] log likelihood: -6238.281093
EM: Round [199] log likelihood: -6238.278380
EM: Round [200] log likelihood: -6238.275690
EM: Round [201] log likelihood: -6238.273022
EM: Round [202] log likelihood: -6238.270377
EM: Round [203] log likelihood: -6238.267753
EM: Round [204] log likelihood: -6238.265150
EM: Round [205] log likelihood: -6238.262568
EM: Round [206] log likelihood: -6238.260007
EM: Round [207] log likelihood: -6238.257466
EM: Round [208] log likelihood: -6238.254944
EM: Round [209] log likelihood: -6238.252441
EM: Round [210] log likelihood: -6238.249958
EM: Round [211] log likelihood: -6238.247493
EM: Round [212] log likelihood: -6238.245046
EM: Round [213] log likelihood: -6238.242617
EM: Round [214] log likelihood: -6238.240206
EM: Round [215] log likelihood: -6238.237812
EM: Round [216] log likelihood: -6238.235435
EM: Round [217] log likelihood: -6238.233074
EM: Round [218] log likelihood: -6238.230730
EM: Round [219] log likelihood: -6238.228402
EM: Round [220] log likelihood: -6238.226090
EM: Round [221] log likelihood: -6238.223793
EM: Round [222] log likelihood: -6238.221511
EM: Round [223] log likelihood: -6238.219245
EM: Round [224] log likelihood: -6238.216993
EM: Round [225] log likelihood: -6238.214755
EM: Round [226] log likelihood: -6238.212532
EM: Round [227] log likelihood: -6238.210323
EM: Round [228] log likelihood: -6238.208127
EM: Round [229] log likelihood: -6238.205945
EM: Round [230] log likelihood: -6238.203776
EM: Round [231] log likelihood: -6238.201621
EM: Round [232] log likelihood: -6238.199478
EM: Round [233] log likelihood: -6238.197348
EM: Round [234] log likelihood: -6238.195230
EM: Round [235] log likelihood: -6238.193125
EM: Round [236] log likelihood: -6238.191032
EM: Round [237] log likelihood: -6238.188950
EM: Round [238] log likelihood: -6238.186880
EM: Round [239] log likelihood: -6238.184822
EM: Round [240] log likelihood: -6238.182775
EM: Round [241] log likelihood: -6238.180739
EM: Round [242] log likelihood: -6238.178715
EM: Round [243] log likelihood: -6238.176701
EM: Round [244] log likelihood: -6238.174698
EM: Round [245] log likelihood: -6238.172705
EM: Round [246] log likelihood: -6238.170722
EM: Round [247] log likelihood: -6238.168750
EM: Round [248] log likelihood: -6238.166788
EM: Round [249] log likelihood: -6238.164836
EM: Round [250] log likelihood: -6238.162894
EM: Round [251] log likelihood: -6238.160961
EM: Round [252] log likelihood: -6238.159038
EM: Round [253] log likelihood: -6238.157124
EM: Round [254] log likelihood: -6238.155219
EM: Round [255] log likelihood: -6238.153324
EM: Round [256] log likelihood: -6238.151438
EM: Round [257] log likelihood: -6238.149560
EM: Round [258] log likelihood: -6238.147691
EM: Round [259] log likelihood: -6238.145831
EM: Round [260] log likelihood: -6238.143980
EM: Round [261] log likelihood: -6238.142136
EM: Round [262] log likelihood: -6238.140302
EM: Round [263] log likelihood: -6238.138475
EM: Round [264] log likelihood: -6238.136657
EM: Round [265] log likelihood: -6238.134846
EM: Round [266] log likelihood: -6238.133044
EM: Round [267] log likelihood: -6238.131249
EM: Round [268] log likelihood: -6238.129462
EM: Round [269] log likelihood: -6238.127683
EM: Round [270] log likelihood: -6238.125911
EM: Round [271] log likelihood: -6238.124146
EM: Round [272] log likelihood: -6238.122389
EM: Round [273] log likelihood: -6238.120640
EM: Round [274] log likelihood: -6238.118897
EM: Round [275] log likelihood: -6238.117162
EM: Round [276] log likelihood: -6238.115434
EM: Round [277] log likelihood: -6238.113712
EM: Round [278] log likelihood: -6238.111998
EM: Round [279] log likelihood: -6238.110290
EM: Round [280] log likelihood: -6238.108589
EM: Round [281] log likelihood: -6238.106895
EM: Round [282] log likelihood: -6238.105208
EM: Round [283] log likelihood: -6238.103526
EM: Round [284] log likelihood: -6238.101852
EM: Round [285] log likelihood: -6238.100184
EM: Round [286] log likelihood: -6238.098522
EM: Round [287] log likelihood: -6238.096866
EM: Round [288] log likelihood: -6238.095216
EM: Round [289] log likelihood: -6238.093573
EM: Round [290] log likelihood: -6238.091936
EM: Round [291] log likelihood: -6238.090305
EM: Round [292] log likelihood: -6238.088679
EM: Round [293] log likelihood: -6238.087060
EM: Round [294] log likelihood: -6238.085447
EM: Round [295] log likelihood: -6238.083839
EM: Round [296] log likelihood: -6238.082237
EM: Round [297] log likelihood: -6238.080641
EM: Round [298] log likelihood: -6238.079050
EM: Round [299] log likelihood: -6238.077465
EM: Round [300] log likelihood: -6238.075885
EM: Round [301] log likelihood: -6238.074311
EM: Round [302] log likelihood: -6238.072743
EM: Round [303] log likelihood: -6238.071179
EM: Round [304] log likelihood: -6238.069622
EM: Round [305] log likelihood: -6238.068069
EM: Round [306] log likelihood: -6238.066522
EM: Round [307] log likelihood: -6238.064980
EM: Round [308] log likelihood: -6238.063443
EM: Round [309] log likelihood: -6238.061911
EM: Round [310] log likelihood: -6238.060384
EM: Round [311] log likelihood: -6238.058862
EM: Round [312] log likelihood: -6238.057346
EM: Round [313] log likelihood: -6238.055834
EM: Round [314] log likelihood: -6238.054327
EM: Round [315] log likelihood: -6238.052825
EM: Round [316] log likelihood: -6238.051328
EM: Round [317] log likelihood: -6238.049836
EM: Round [318] log likelihood: -6238.048349
EM: Round [319] log likelihood: -6238.046866
EM: Round [320] log likelihood: -6238.045388
EM: Round [321] log likelihood: -6238.043914
EM: Round [322] log likelihood: -6238.042446
EM: Round [323] log likelihood: -6238.040982
EM: Round [324] log likelihood: -6238.039522
EM: Round [325] log likelihood: -6238.038067
EM: Round [326] log likelihood: -6238.036616
EM: Round [327] log likelihood: -6238.035170
EM: Round [328] log likelihood: -6238.033729
EM: Round [329] log likelihood: -6238.032292
EM: Round [330] log likelihood: -6238.030859
EM: Round [331] log likelihood: -6238.029430
EM: Round [332] log likelihood: -6238.028006
EM: Round [333] log likelihood: -6238.026586
EM: Round [334] log likelihood: -6238.025171
EM: Round [335] log likelihood: -6238.023759
EM: Round [336] log likelihood: -6238.022352
EM: Round [337] log likelihood: -6238.020949
EM: Round [338] log likelihood: -6238.019551
EM: Round [339] log likelihood: -6238.018156
EM: Round [340] log likelihood: -6238.016765
EM: Round [341] log likelihood: -6238.015379
EM: Round [342] log likelihood: -6238.013996
EM: Round [343] log likelihood: -6238.012618
EM: Round [344] log likelihood: -6238.011244
EM: Round [345] log likelihood: -6238.009873
EM: Round [346] log likelihood: -6238.008507
EM: Round [347] log likelihood: -6238.007144
EM: Round [348] log likelihood: -6238.005786
EM: Round [349] log likelihood: -6238.004431
EM: Round [350] log likelihood: -6238.003080
EM: Round [351] log likelihood: -6238.001733
EM: Round [352] log likelihood: -6238.000390
EM: Round [353] log likelihood: -6237.999050
EM: Round [354] log likelihood: -6237.997715
EM: Round [355] log likelihood: -6237.996383
EM: Round [356] log likelihood: -6237.995055
EM: Round [357] log likelihood: -6237.993730
EM: Round [358] log likelihood: -6237.992410
EM: Round [359] log likelihood: -6237.991092
EM: Round [360] log likelihood: -6237.989779
EM: Round [361] log likelihood: -6237.988469
EM: Round [362] log likelihood: -6237.987163
EM: Round [363] log likelihood: -6237.985861
EM: Round [364] log likelihood: -6237.984562
EM: Round [365] log likelihood: -6237.983266
EM: Round [366] log likelihood: -6237.981974
EM: Round [367] log likelihood: -6237.980686
EM: Round [368] log likelihood: -6237.979401
EM: Round [369] log likelihood: -6237.978120
EM: Round [370] log likelihood: -6237.976842
EM: Round [371] log likelihood: -6237.975567
EM: Round [372] log likelihood: -6237.974296
EM: Round [373] log likelihood: -6237.973029
EM: Round [374] log likelihood: -6237.971765
EM: Round [375] log likelihood: -6237.970504
EM: Round [376] log likelihood: -6237.969246
EM: Round [377] log likelihood: -6237.967992
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EM: Round [834] log likelihood: -6237.610741
EM: Round [835] log likelihood: -6237.610261
EM: Round [836] log likelihood: -6237.609782
EM: Round [837] log likelihood: -6237.609304
EM: Round [838] log likelihood: -6237.608826
EM: Round [839] log likelihood: -6237.608350
EM: Round [840] log likelihood: -6237.607874
EM: Round [841] log likelihood: -6237.607399
EM: Round [842] log likelihood: -6237.606925
EM: Round [843] log likelihood: -6237.606452
EM: Round [844] log likelihood: -6237.605979
EM: Round [845] log likelihood: -6237.605508
EM: Round [846] log likelihood: -6237.605037
EM: Round [847] log likelihood: -6237.604567
EM: Round [848] log likelihood: -6237.604098
EM: Round [849] log likelihood: -6237.603630
EM: Round [850] log likelihood: -6237.603163
EM: Round [851] log likelihood: -6237.602696
EM: Round [852] log likelihood: -6237.602230
EM: Round [853] log likelihood: -6237.601765
EM: Round [854] log likelihood: -6237.601301
EM: Round [855] log likelihood: -6237.600838
EM: Round [856] log likelihood: -6237.600376
EM: Round [857] log likelihood: -6237.599914
EM: Round [858] log likelihood: -6237.599453
EM: Round [859] log likelihood: -6237.598993
EM: Round [860] log likelihood: -6237.598534
EM: Round [861] log likelihood: -6237.598075
EM: Round [862] log likelihood: -6237.597618
EM: Round [863] log likelihood: -6237.597161
EM: Round [864] log likelihood: -6237.596705
EM: Round [865] log likelihood: -6237.596250
EM: Round [866] log likelihood: -6237.595796
EM: Round [867] log likelihood: -6237.595342
EM: Round [868] log likelihood: -6237.594889
EM: Round [869] log likelihood: -6237.594437
EM: Round [870] log likelihood: -6237.593986
EM: Round [871] log likelihood: -6237.593536
EM: Round [872] log likelihood: -6237.593086
EM: Round [873] log likelihood: -6237.592637
EM: Round [874] log likelihood: -6237.592189
EM: Round [875] log likelihood: -6237.591742
EM: Round [876] log likelihood: -6237.591295
EM: Round [877] log likelihood: -6237.590850
EM: Round [878] log likelihood: -6237.590405
EM: Round [879] log likelihood: -6237.589961
EM: Round [880] log likelihood: -6237.589517
EM: Round [881] log likelihood: -6237.589075
EM: Round [882] log likelihood: -6237.588633
EM: Round [883] log likelihood: -6237.588192
EM: Round [884] log likelihood: -6237.587752
EM: Round [885] log likelihood: -6237.587312
EM: Round [886] log likelihood: -6237.586874
EM: Round [887] log likelihood: -6237.586436
EM: Round [888] log likelihood: -6237.585998
EM: Round [889] log likelihood: -6237.585562
EM: Round [890] log likelihood: -6237.585126
EM: Round [891] log likelihood: -6237.584691
EM: Round [892] log likelihood: -6237.584257
EM: Round [893] log likelihood: -6237.583824
EM: Round [894] log likelihood: -6237.583391
EM: Round [895] log likelihood: -6237.582959
EM: Round [896] log likelihood: -6237.582528
EM: Round [897] log likelihood: -6237.582098
EM: Round [898] log likelihood: -6237.581668
EM: Round [899] log likelihood: -6237.581239
EM: Round [900] log likelihood: -6237.580811
EM: Round [901] log likelihood: -6237.580383
EM: Round [902] log likelihood: -6237.579957
EM: Round [903] log likelihood: -6237.579531
EM: Round [904] log likelihood: -6237.579105
EM: Round [905] log likelihood: -6237.578681
EM: Round [906] log likelihood: -6237.578257
EM: Round [907] log likelihood: -6237.577834
EM: Round [908] log likelihood: -6237.577412
EM: Round [909] log likelihood: -6237.576990
EM: Round [910] log likelihood: -6237.576569
EM: Round [911] log likelihood: -6237.576149
EM: Round [912] log likelihood: -6237.575730
EM: Round [913] log likelihood: -6237.575311
EM: Round [914] log likelihood: -6237.574893
EM: Round [915] log likelihood: -6237.574476
EM: Round [916] log likelihood: -6237.574059
EM: Round [917] log likelihood: -6237.573644
EM: Round [918] log likelihood: -6237.573229
EM: Round [919] log likelihood: -6237.572814
EM: Round [920] log likelihood: -6237.572401
EM: Round [921] log likelihood: -6237.571988
EM: Round [922] log likelihood: -6237.571575
EM: Round [923] log likelihood: -6237.571164
EM: Round [924] log likelihood: -6237.570753
EM: Round [925] log likelihood: -6237.570343
EM: Round [926] log likelihood: -6237.569933
EM: Round [927] log likelihood: -6237.569525
EM: Round [928] log likelihood: -6237.569117
EM: Round [929] log likelihood: -6237.568709
EM: Round [930] log likelihood: -6237.568303
EM: Round [931] log likelihood: -6237.567897
EM: Round [932] log likelihood: -6237.567492
EM: Round [933] log likelihood: -6237.567087
EM: Round [934] log likelihood: -6237.566683
EM: Round [935] log likelihood: -6237.566280
EM: Round [936] log likelihood: -6237.565878
EM: Round [937] log likelihood: -6237.565476
EM: Round [938] log likelihood: -6237.565075
EM: Round [939] log likelihood: -6237.564674
EM: Round [940] log likelihood: -6237.564275
EM: Round [941] log likelihood: -6237.563875
EM: Round [942] log likelihood: -6237.563477
EM: Round [943] log likelihood: -6237.563079
EM: Round [944] log likelihood: -6237.562682
EM: Round [945] log likelihood: -6237.562286
EM: Round [946] log likelihood: -6237.561890
EM: Round [947] log likelihood: -6237.561495
EM: Round [948] log likelihood: -6237.561101
EM: Round [949] log likelihood: -6237.560707
EM: Round [950] log likelihood: -6237.560314
EM: Round [951] log likelihood: -6237.559922
EM: Round [952] log likelihood: -6237.559530
EM: Round [953] log likelihood: -6237.559139
EM: Round [954] log likelihood: -6237.558749
EM: Round [955] log likelihood: -6237.558359
EM: Round [956] log likelihood: -6237.557970
EM: Round [957] log likelihood: -6237.557582
EM: Round [958] log likelihood: -6237.557194
EM: Round [959] log likelihood: -6237.556807
EM: Round [960] log likelihood: -6237.556421
EM: Round [961] log likelihood: -6237.556035
EM: Round [962] log likelihood: -6237.555650
EM: Round [963] log likelihood: -6237.555265
EM: Round [964] log likelihood: -6237.554882
EM: Round [965] log likelihood: -6237.554499
EM: Round [966] log likelihood: -6237.554116
EM: Round [967] log likelihood: -6237.553734
EM: Round [968] log likelihood: -6237.553353
EM: Round [969] log likelihood: -6237.552972
EM: Round [970] log likelihood: -6237.552592
EM: Round [971] log likelihood: -6237.552213
EM: Round [972] log likelihood: -6237.551835
EM: Round [973] log likelihood: -6237.551457
EM: Round [974] log likelihood: -6237.551079
EM: Round [975] log likelihood: -6237.550702
EM: Round [976] log likelihood: -6237.550326
EM: Round [977] log likelihood: -6237.549951
EM: Round [978] log likelihood: -6237.549576
EM: Round [979] log likelihood: -6237.549202
EM: Round [980] log likelihood: -6237.548828
EM: Round [981] log likelihood: -6237.548455
EM: Round [982] log likelihood: -6237.548083
EM: Round [983] log likelihood: -6237.547711
EM: Round [984] log likelihood: -6237.547340
EM: Round [985] log likelihood: -6237.546970
EM: Round [986] log likelihood: -6237.546600
EM: Round [987] log likelihood: -6237.546230
EM: Round [988] log likelihood: -6237.545862
EM: Round [989] log likelihood: -6237.545494
EM: Round [990] log likelihood: -6237.545126
EM: Round [991] log likelihood: -6237.544760
EM: Round [992] log likelihood: -6237.544394
EM: Round [993] log likelihood: -6237.544028
EM: Round [994] log likelihood: -6237.543663
EM: Round [995] log likelihood: -6237.543299
EM: Round [996] log likelihood: -6237.542935
EM: Round [997] log likelihood: -6237.542572
EM: Round [998] log likelihood: -6237.542209
EM: Round [999] log likelihood: -6237.541847
EM: Round [1000] log likelihood: -6237.541486
EM: Round [1001] log likelihood: -6237.541125
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir
-done, see /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4621.731113
EM: Round [1] log likelihood: -4621.546433
EM: Round [2] log likelihood: -4621.537414
EM: Round [3] log likelihood: -4621.528604
EM: Round [4] log likelihood: -4621.519883
EM: Round [5] log likelihood: -4621.511248
EM: Round [6] log likelihood: -4621.502698
EM: Round [7] log likelihood: -4621.494231
EM: Round [8] log likelihood: -4621.485847
EM: Round [9] log likelihood: -4621.477543
EM: Round [10] log likelihood: -4621.469318
EM: Round [11] log likelihood: -4621.461171
EM: Round [12] log likelihood: -4621.453100
EM: Round [13] log likelihood: -4621.445104
EM: Round [14] log likelihood: -4621.437182
EM: Round [15] log likelihood: -4621.429332
EM: Round [16] log likelihood: -4621.421554
EM: Round [17] log likelihood: -4621.413845
EM: Round [18] log likelihood: -4621.406206
EM: Round [19] log likelihood: -4621.398634
EM: Round [20] log likelihood: -4621.391129
EM: Round [21] log likelihood: -4621.383690
EM: Round [22] log likelihood: -4621.376315
EM: Round [23] log likelihood: -4621.369003
EM: Round [24] log likelihood: -4621.361754
EM: Round [25] log likelihood: -4621.354567
EM: Round [26] log likelihood: -4621.347440
EM: Round [27] log likelihood: -4621.340373
EM: Round [28] log likelihood: -4621.333364
EM: Round [29] log likelihood: -4621.326414
EM: Round [30] log likelihood: -4621.319520
EM: Round [31] log likelihood: -4621.312682
EM: Round [32] log likelihood: -4621.305900
EM: Round [33] log likelihood: -4621.299172
EM: Round [34] log likelihood: -4621.292498
EM: Round [35] log likelihood: -4621.285876
EM: Round [36] log likelihood: -4621.279307
EM: Round [37] log likelihood: -4621.272789
EM: Round [38] log likelihood: -4621.266322
EM: Round [39] log likelihood: -4621.259904
EM: Round [40] log likelihood: -4621.253536
EM: Round [41] log likelihood: -4621.247216
EM: Round [42] log likelihood: -4621.240944
EM: Round [43] log likelihood: -4621.234720
EM: Round [44] log likelihood: -4621.228542
EM: Round [45] log likelihood: -4621.222409
EM: Round [46] log likelihood: -4621.216322
EM: Round [47] log likelihood: -4621.210280
EM: Round [48] log likelihood: -4621.204282
EM: Round [49] log likelihood: -4621.198328
EM: Round [50] log likelihood: -4621.192416
EM: Round [51] log likelihood: -4621.186547
EM: Round [52] log likelihood: -4621.180719
EM: Round [53] log likelihood: -4621.174933
EM: Round [54] log likelihood: -4621.169188
EM: Round [55] log likelihood: -4621.163482
EM: Round [56] log likelihood: -4621.157817
EM: Round [57] log likelihood: -4621.152191
EM: Round [58] log likelihood: -4621.146604
EM: Round [59] log likelihood: -4621.141054
EM: Round [60] log likelihood: -4621.135543
EM: Round [61] log likelihood: -4621.130069
EM: Round [62] log likelihood: -4621.124632
EM: Round [63] log likelihood: -4621.119231
EM: Round [64] log likelihood: -4621.113867
EM: Round [65] log likelihood: -4621.108537
EM: Round [66] log likelihood: -4621.103243
EM: Round [67] log likelihood: -4621.097984
EM: Round [68] log likelihood: -4621.092759
EM: Round [69] log likelihood: -4621.087568
EM: Round [70] log likelihood: -4621.082411
EM: Round [71] log likelihood: -4621.077286
EM: Round [72] log likelihood: -4621.072195
EM: Round [73] log likelihood: -4621.067135
EM: Round [74] log likelihood: -4621.062108
EM: Round [75] log likelihood: -4621.057113
EM: Round [76] log likelihood: -4621.052148
EM: Round [77] log likelihood: -4621.047215
EM: Round [78] log likelihood: -4621.042312
EM: Round [79] log likelihood: -4621.037440
EM: Round [80] log likelihood: -4621.032597
EM: Round [81] log likelihood: -4621.027785
EM: Round [82] log likelihood: -4621.023001
EM: Round [83] log likelihood: -4621.018246
EM: Round [84] log likelihood: -4621.013520
EM: Round [85] log likelihood: -4621.008823
EM: Round [86] log likelihood: -4621.004153
EM: Round [87] log likelihood: -4620.999511
EM: Round [88] log likelihood: -4620.994897
EM: Round [89] log likelihood: -4620.990309
EM: Round [90] log likelihood: -4620.985749
EM: Round [91] log likelihood: -4620.981215
EM: Round [92] log likelihood: -4620.976708
EM: Round [93] log likelihood: -4620.972227
EM: Round [94] log likelihood: -4620.967771
EM: Round [95] log likelihood: -4620.963341
EM: Round [96] log likelihood: -4620.958936
EM: Round [97] log likelihood: -4620.954557
EM: Round [98] log likelihood: -4620.950202
EM: Round [99] log likelihood: -4620.945871
EM: Round [100] log likelihood: -4620.941565
EM: Round [101] log likelihood: -4620.937283
EM: Round [102] log likelihood: -4620.933025
EM: Round [103] log likelihood: -4620.928790
EM: Round [104] log likelihood: -4620.924579
EM: Round [105] log likelihood: -4620.920390
EM: Round [106] log likelihood: -4620.916225
EM: Round [107] log likelihood: -4620.912082
EM: Round [108] log likelihood: -4620.907962
EM: Round [109] log likelihood: -4620.903864
EM: Round [110] log likelihood: -4620.899788
EM: Round [111] log likelihood: -4620.895734
EM: Round [112] log likelihood: -4620.891701
EM: Round [113] log likelihood: -4620.887690
EM: Round [114] log likelihood: -4620.883701
EM: Round [115] log likelihood: -4620.879732
EM: Round [116] log likelihood: -4620.875784
EM: Round [117] log likelihood: -4620.871856
EM: Round [118] log likelihood: -4620.867949
EM: Round [119] log likelihood: -4620.864063
EM: Round [120] log likelihood: -4620.860196
EM: Round [121] log likelihood: -4620.856350
EM: Round [122] log likelihood: -4620.852523
EM: Round [123] log likelihood: -4620.848715
EM: Round [124] log likelihood: -4620.844927
EM: Round [125] log likelihood: -4620.841159
EM: Round [126] log likelihood: -4620.837409
EM: Round [127] log likelihood: -4620.833678
EM: Round [128] log likelihood: -4620.829966
EM: Round [129] log likelihood: -4620.826272
EM: Round [130] log likelihood: -4620.822597
EM: Round [131] log likelihood: -4620.818940
EM: Round [132] log likelihood: -4620.815301
EM: Round [133] log likelihood: -4620.811680
EM: Round [134] log likelihood: -4620.808077
EM: Round [135] log likelihood: -4620.804491
EM: Round [136] log likelihood: -4620.800923
EM: Round [137] log likelihood: -4620.797372
EM: Round [138] log likelihood: -4620.793838
EM: Round [139] log likelihood: -4620.790321
EM: Round [140] log likelihood: -4620.786822
EM: Round [141] log likelihood: -4620.783339
EM: Round [142] log likelihood: -4620.779872
EM: Round [143] log likelihood: -4620.776422
EM: Round [144] log likelihood: -4620.772988
EM: Round [145] log likelihood: -4620.769571
EM: Round [146] log likelihood: -4620.766170
EM: Round [147] log likelihood: -4620.762784
EM: Round [148] log likelihood: -4620.759415
EM: Round [149] log likelihood: -4620.756061
EM: Round [150] log likelihood: -4620.752722
EM: Round [151] log likelihood: -4620.749399
EM: Round [152] log likelihood: -4620.746092
EM: Round [153] log likelihood: -4620.742799
EM: Round [154] log likelihood: -4620.739522
EM: Round [155] log likelihood: -4620.736260
EM: Round [156] log likelihood: -4620.733012
EM: Round [157] log likelihood: -4620.729779
EM: Round [158] log likelihood: -4620.726561
EM: Round [159] log likelihood: -4620.723357
EM: Round [160] log likelihood: -4620.720168
EM: Round [161] log likelihood: -4620.716993
EM: Round [162] log likelihood: -4620.713832
EM: Round [163] log likelihood: -4620.710685
EM: Round [164] log likelihood: -4620.707552
EM: Round [165] log likelihood: -4620.704433
EM: Round [166] log likelihood: -4620.701328
EM: Round [167] log likelihood: -4620.698236
EM: Round [168] log likelihood: -4620.695158
EM: Round [169] log likelihood: -4620.692094
EM: Round [170] log likelihood: -4620.689042
EM: Round [171] log likelihood: -4620.686004
EM: Round [172] log likelihood: -4620.682979
EM: Round [173] log likelihood: -4620.679968
EM: Round [174] log likelihood: -4620.676969
EM: Round [175] log likelihood: -4620.673983
EM: Round [176] log likelihood: -4620.671009
EM: Round [177] log likelihood: -4620.668049
EM: Round [178] log likelihood: -4620.665101
EM: Round [179] log likelihood: -4620.662165
EM: Round [180] log likelihood: -4620.659242
EM: Round [181] log likelihood: -4620.656331
EM: Round [182] log likelihood: -4620.653433
EM: Round [183] log likelihood: -4620.650546
EM: Round [184] log likelihood: -4620.647672
EM: Round [185] log likelihood: -4620.644809
EM: Round [186] log likelihood: -4620.641959
EM: Round [187] log likelihood: -4620.639120
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EM: Round [650] log likelihood: -4619.953745
EM: Round [651] log likelihood: -4619.952965
EM: Round [652] log likelihood: -4619.952187
EM: Round [653] log likelihood: -4619.951411
EM: Round [654] log likelihood: -4619.950636
EM: Round [655] log likelihood: -4619.949863
EM: Round [656] log likelihood: -4619.949092
EM: Round [657] log likelihood: -4619.948322
EM: Round [658] log likelihood: -4619.947554
EM: Round [659] log likelihood: -4619.946788
EM: Round [660] log likelihood: -4619.946023
EM: Round [661] log likelihood: -4619.945259
EM: Round [662] log likelihood: -4619.944497
EM: Round [663] log likelihood: -4619.943737
EM: Round [664] log likelihood: -4619.942978
EM: Round [665] log likelihood: -4619.942221
EM: Round [666] log likelihood: -4619.941465
EM: Round [667] log likelihood: -4619.940711
EM: Round [668] log likelihood: -4619.939959
EM: Round [669] log likelihood: -4619.939208
EM: Round [670] log likelihood: -4619.938459
EM: Round [671] log likelihood: -4619.937711
EM: Round [672] log likelihood: -4619.936964
EM: Round [673] log likelihood: -4619.936220
EM: Round [674] log likelihood: -4619.935476
EM: Round [675] log likelihood: -4619.934735
EM: Round [676] log likelihood: -4619.933994
EM: Round [677] log likelihood: -4619.933256
EM: Round [678] log likelihood: -4619.932518
EM: Round [679] log likelihood: -4619.931783
EM: Round [680] log likelihood: -4619.931048
EM: Round [681] log likelihood: -4619.930316
EM: Round [682] log likelihood: -4619.929584
EM: Round [683] log likelihood: -4619.928855
EM: Round [684] log likelihood: -4619.928126
EM: Round [685] log likelihood: -4619.927400
EM: Round [686] log likelihood: -4619.926674
EM: Round [687] log likelihood: -4619.925951
EM: Round [688] log likelihood: -4619.925228
EM: Round [689] log likelihood: -4619.924507
EM: Round [690] log likelihood: -4619.923788
EM: Round [691] log likelihood: -4619.923070
EM: Round [692] log likelihood: -4619.922353
EM: Round [693] log likelihood: -4619.921638
EM: Round [694] log likelihood: -4619.920924
EM: Round [695] log likelihood: -4619.920212
EM: Round [696] log likelihood: -4619.919501
EM: Round [697] log likelihood: -4619.918792
EM: Round [698] log likelihood: -4619.918084
EM: Round [699] log likelihood: -4619.917378
EM: Round [700] log likelihood: -4619.916673
EM: Round [701] log likelihood: -4619.915969
EM: Round [702] log likelihood: -4619.915267
EM: Round [703] log likelihood: -4619.914566
EM: Round [704] log likelihood: -4619.913866
EM: Round [705] log likelihood: -4619.913168
EM: Round [706] log likelihood: -4619.912472
EM: Round [707] log likelihood: -4619.911776
EM: Round [708] log likelihood: -4619.911082
EM: Round [709] log likelihood: -4619.910390
EM: Round [710] log likelihood: -4619.909699
EM: Round [711] log likelihood: -4619.909009
EM: Round [712] log likelihood: -4619.908321
EM: Round [713] log likelihood: -4619.907634
EM: Round [714] log likelihood: -4619.906948
EM: Round [715] log likelihood: -4619.906264
EM: Round [716] log likelihood: -4619.905581
EM: Round [717] log likelihood: -4619.904899
EM: Round [718] log likelihood: -4619.904219
EM: Round [719] log likelihood: -4619.903540
EM: Round [720] log likelihood: -4619.902863
EM: Round [721] log likelihood: -4619.902187
EM: Round [722] log likelihood: -4619.901512
EM: Round [723] log likelihood: -4619.900838
EM: Round [724] log likelihood: -4619.900166
EM: Round [725] log likelihood: -4619.899495
EM: Round [726] log likelihood: -4619.898826
EM: Round [727] log likelihood: -4619.898158
EM: Round [728] log likelihood: -4619.897491
EM: Round [729] log likelihood: -4619.896825
EM: Round [730] log likelihood: -4619.896161
EM: Round [731] log likelihood: -4619.895498
EM: Round [732] log likelihood: -4619.894837
EM: Round [733] log likelihood: -4619.894176
EM: Round [734] log likelihood: -4619.893517
EM: Round [735] log likelihood: -4619.892859
EM: Round [736] log likelihood: -4619.892203
EM: Round [737] log likelihood: -4619.891548
EM: Round [738] log likelihood: -4619.890894
EM: Round [739] log likelihood: -4619.890241
EM: Round [740] log likelihood: -4619.889590
EM: Round [741] log likelihood: -4619.888940
EM: Round [742] log likelihood: -4619.888291
EM: Round [743] log likelihood: -4619.887644
EM: Round [744] log likelihood: -4619.886997
EM: Round [745] log likelihood: -4619.886352
EM: Round [746] log likelihood: -4619.885708
EM: Round [747] log likelihood: -4619.885066
EM: Round [748] log likelihood: -4619.884425
EM: Round [749] log likelihood: -4619.883785
EM: Round [750] log likelihood: -4619.883146
EM: Round [751] log likelihood: -4619.882508
EM: Round [752] log likelihood: -4619.881872
EM: Round [753] log likelihood: -4619.881237
EM: Round [754] log likelihood: -4619.880603
EM: Round [755] log likelihood: -4619.879971
EM: Round [756] log likelihood: -4619.879339
EM: Round [757] log likelihood: -4619.878709
EM: Round [758] log likelihood: -4619.878080
EM: Round [759] log likelihood: -4619.877452
EM: Round [760] log likelihood: -4619.876826
EM: Round [761] log likelihood: -4619.876201
EM: Round [762] log likelihood: -4619.875577
EM: Round [763] log likelihood: -4619.874954
EM: Round [764] log likelihood: -4619.874332
EM: Round [765] log likelihood: -4619.873711
EM: Round [766] log likelihood: -4619.873092
EM: Round [767] log likelihood: -4619.872474
EM: Round [768] log likelihood: -4619.871857
EM: Round [769] log likelihood: -4619.871241
EM: Round [770] log likelihood: -4619.870627
EM: Round [771] log likelihood: -4619.870013
EM: Round [772] log likelihood: -4619.869401
EM: Round [773] log likelihood: -4619.868790
EM: Round [774] log likelihood: -4619.868180
EM: Round [775] log likelihood: -4619.867572
EM: Round [776] log likelihood: -4619.866964
EM: Round [777] log likelihood: -4619.866358
EM: Round [778] log likelihood: -4619.865752
EM: Round [779] log likelihood: -4619.865148
EM: Round [780] log likelihood: -4619.864546
EM: Round [781] log likelihood: -4619.863944
EM: Round [782] log likelihood: -4619.863343
EM: Round [783] log likelihood: -4619.862744
EM: Round [784] log likelihood: -4619.862145
EM: Round [785] log likelihood: -4619.861548
EM: Round [786] log likelihood: -4619.860952
EM: Round [787] log likelihood: -4619.860357
EM: Round [788] log likelihood: -4619.859763
EM: Round [789] log likelihood: -4619.859171
EM: Round [790] log likelihood: -4619.858579
EM: Round [791] log likelihood: -4619.857989
EM: Round [792] log likelihood: -4619.857399
EM: Round [793] log likelihood: -4619.856811
EM: Round [794] log likelihood: -4619.856224
EM: Round [795] log likelihood: -4619.855638
EM: Round [796] log likelihood: -4619.855053
EM: Round [797] log likelihood: -4619.854469
EM: Round [798] log likelihood: -4619.853887
EM: Round [799] log likelihood: -4619.853305
EM: Round [800] log likelihood: -4619.852725
EM: Round [801] log likelihood: -4619.852145
EM: Round [802] log likelihood: -4619.851567
EM: Round [803] log likelihood: -4619.850990
EM: Round [804] log likelihood: -4619.850414
EM: Round [805] log likelihood: -4619.849839
EM: Round [806] log likelihood: -4619.849265
EM: Round [807] log likelihood: -4619.848692
EM: Round [808] log likelihood: -4619.848120
EM: Round [809] log likelihood: -4619.847549
EM: Round [810] log likelihood: -4619.846980
EM: Round [811] log likelihood: -4619.846411
EM: Round [812] log likelihood: -4619.845843
EM: Round [813] log likelihood: -4619.845277
EM: Round [814] log likelihood: -4619.844711
EM: Round [815] log likelihood: -4619.844147
EM: Round [816] log likelihood: -4619.843584
EM: Round [817] log likelihood: -4619.843022
EM: Round [818] log likelihood: -4619.842460
EM: Round [819] log likelihood: -4619.841900
EM: Round [820] log likelihood: -4619.841341
EM: Round [821] log likelihood: -4619.840783
EM: Round [822] log likelihood: -4619.840226
EM: Round [823] log likelihood: -4619.839670
EM: Round [824] log likelihood: -4619.839115
EM: Round [825] log likelihood: -4619.838561
EM: Round [826] log likelihood: -4619.838008
EM: Round [827] log likelihood: -4619.837456
EM: Round [828] log likelihood: -4619.836905
EM: Round [829] log likelihood: -4619.836356
EM: Round [830] log likelihood: -4619.835807
EM: Round [831] log likelihood: -4619.835259
EM: Round [832] log likelihood: -4619.834712
EM: Round [833] log likelihood: -4619.834166
EM: Round [834] log likelihood: -4619.833622
EM: Round [835] log likelihood: -4619.833078
EM: Round [836] log likelihood: -4619.832535
EM: Round [837] log likelihood: -4619.831993
EM: Round [838] log likelihood: -4619.831452
EM: Round [839] log likelihood: -4619.830913
EM: Round [840] log likelihood: -4619.830374
EM: Round [841] log likelihood: -4619.829836
EM: Round [842] log likelihood: -4619.829299
EM: Round [843] log likelihood: -4619.828764
EM: Round [844] log likelihood: -4619.828229
EM: Round [845] log likelihood: -4619.827695
EM: Round [846] log likelihood: -4619.827162
EM: Round [847] log likelihood: -4619.826630
EM: Round [848] log likelihood: -4619.826099
EM: Round [849] log likelihood: -4619.825569
EM: Round [850] log likelihood: -4619.825040
EM: Round [851] log likelihood: -4619.824512
EM: Round [852] log likelihood: -4619.823985
EM: Round [853] log likelihood: -4619.823459
EM: Round [854] log likelihood: -4619.822934
EM: Round [855] log likelihood: -4619.822410
EM: Round [856] log likelihood: -4619.821887
EM: Round [857] log likelihood: -4619.821365
EM: Round [858] log likelihood: -4619.820843
EM: Round [859] log likelihood: -4619.820323
EM: Round [860] log likelihood: -4619.819804
EM: Round [861] log likelihood: -4619.819285
EM: Round [862] log likelihood: -4619.818768
EM: Round [863] log likelihood: -4619.818251
EM: Round [864] log likelihood: -4619.817736
EM: Round [865] log likelihood: -4619.817221
EM: Round [866] log likelihood: -4619.816707
EM: Round [867] log likelihood: -4619.816194
EM: Round [868] log likelihood: -4619.815683
EM: Round [869] log likelihood: -4619.815172
EM: Round [870] log likelihood: -4619.814662
EM: Round [871] log likelihood: -4619.814153
EM: Round [872] log likelihood: -4619.813644
EM: Round [873] log likelihood: -4619.813137
EM: Round [874] log likelihood: -4619.812631
EM: Round [875] log likelihood: -4619.812125
EM: Round [876] log likelihood: -4619.811621
EM: Round [877] log likelihood: -4619.811117
EM: Round [878] log likelihood: -4619.810615
EM: Round [879] log likelihood: -4619.810113
EM: Round [880] log likelihood: -4619.809612
EM: Round [881] log likelihood: -4619.809112
EM: Round [882] log likelihood: -4619.808613
EM: Round [883] log likelihood: -4619.808115
EM: Round [884] log likelihood: -4619.807618
EM: Round [885] log likelihood: -4619.807121
EM: Round [886] log likelihood: -4619.806626
EM: Round [887] log likelihood: -4619.806131
EM: Round [888] log likelihood: -4619.805637
EM: Round [889] log likelihood: -4619.805145
EM: Round [890] log likelihood: -4619.804653
EM: Round [891] log likelihood: -4619.804162
EM: Round [892] log likelihood: -4619.803672
EM: Round [893] log likelihood: -4619.803182
EM: Round [894] log likelihood: -4619.802694
EM: Round [895] log likelihood: -4619.802206
EM: Round [896] log likelihood: -4619.801720
EM: Round [897] log likelihood: -4619.801234
EM: Round [898] log likelihood: -4619.800749
EM: Round [899] log likelihood: -4619.800265
EM: Round [900] log likelihood: -4619.799782
EM: Round [901] log likelihood: -4619.799299
EM: Round [902] log likelihood: -4619.798818
EM: Round [903] log likelihood: -4619.798337
EM: Round [904] log likelihood: -4619.797858
EM: Round [905] log likelihood: -4619.797379
EM: Round [906] log likelihood: -4619.796901
EM: Round [907] log likelihood: -4619.796423
EM: Round [908] log likelihood: -4619.795947
EM: Round [909] log likelihood: -4619.795472
EM: Round [910] log likelihood: -4619.794997
EM: Round [911] log likelihood: -4619.794523
EM: Round [912] log likelihood: -4619.794050
EM: Round [913] log likelihood: -4619.793578
EM: Round [914] log likelihood: -4619.793107
EM: Round [915] log likelihood: -4619.792636
EM: Round [916] log likelihood: -4619.792167
EM: Round [917] log likelihood: -4619.791698
EM: Round [918] log likelihood: -4619.791230
EM: Round [919] log likelihood: -4619.790763
EM: Round [920] log likelihood: -4619.790297
EM: Round [921] log likelihood: -4619.789831
EM: Round [922] log likelihood: -4619.789367
EM: Round [923] log likelihood: -4619.788903
EM: Round [924] log likelihood: -4619.788440
EM: Round [925] log likelihood: -4619.787978
EM: Round [926] log likelihood: -4619.787516
EM: Round [927] log likelihood: -4619.787056
EM: Round [928] log likelihood: -4619.786596
EM: Round [929] log likelihood: -4619.786137
EM: Round [930] log likelihood: -4619.785679
EM: Round [931] log likelihood: -4619.785222
EM: Round [932] log likelihood: -4619.784765
EM: Round [933] log likelihood: -4619.784309
EM: Round [934] log likelihood: -4619.783854
EM: Round [935] log likelihood: -4619.783400
EM: Round [936] log likelihood: -4619.782947
EM: Round [937] log likelihood: -4619.782494
EM: Round [938] log likelihood: -4619.782043
EM: Round [939] log likelihood: -4619.781592
EM: Round [940] log likelihood: -4619.781142
EM: Round [941] log likelihood: -4619.780692
EM: Round [942] log likelihood: -4619.780244
EM: Round [943] log likelihood: -4619.779796
EM: Round [944] log likelihood: -4619.779349
EM: Round [945] log likelihood: -4619.778903
EM: Round [946] log likelihood: -4619.778457
EM: Round [947] log likelihood: -4619.778013
EM: Round [948] log likelihood: -4619.777569
EM: Round [949] log likelihood: -4619.777126
EM: Round [950] log likelihood: -4619.776683
EM: Round [951] log likelihood: -4619.776242
EM: Round [952] log likelihood: -4619.775801
EM: Round [953] log likelihood: -4619.775361
EM: Round [954] log likelihood: -4619.774922
EM: Round [955] log likelihood: -4619.774483
EM: Round [956] log likelihood: -4619.774046
EM: Round [957] log likelihood: -4619.773609
EM: Round [958] log likelihood: -4619.773172
EM: Round [959] log likelihood: -4619.772737
EM: Round [960] log likelihood: -4619.772302
EM: Round [961] log likelihood: -4619.771868
EM: Round [962] log likelihood: -4619.771435
EM: Round [963] log likelihood: -4619.771003
EM: Round [964] log likelihood: -4619.770571
EM: Round [965] log likelihood: -4619.770140
EM: Round [966] log likelihood: -4619.769710
EM: Round [967] log likelihood: -4619.769281
EM: Round [968] log likelihood: -4619.768852
EM: Round [969] log likelihood: -4619.768424
EM: Round [970] log likelihood: -4619.767997
EM: Round [971] log likelihood: -4619.767570
EM: Round [972] log likelihood: -4619.767145
EM: Round [973] log likelihood: -4619.766720
EM: Round [974] log likelihood: -4619.766295
EM: Round [975] log likelihood: -4619.765872
EM: Round [976] log likelihood: -4619.765449
EM: Round [977] log likelihood: -4619.765027
EM: Round [978] log likelihood: -4619.764606
EM: Round [979] log likelihood: -4619.764185
EM: Round [980] log likelihood: -4619.763765
EM: Round [981] log likelihood: -4619.763346
EM: Round [982] log likelihood: -4619.762927
EM: Round [983] log likelihood: -4619.762510
EM: Round [984] log likelihood: -4619.762093
EM: Round [985] log likelihood: -4619.761676
EM: Round [986] log likelihood: -4619.761261
EM: Round [987] log likelihood: -4619.760846
EM: Round [988] log likelihood: -4619.760432
EM: Round [989] log likelihood: -4619.760018
EM: Round [990] log likelihood: -4619.759606
EM: Round [991] log likelihood: -4619.759194
EM: Round [992] log likelihood: -4619.758782
EM: Round [993] log likelihood: -4619.758372
EM: Round [994] log likelihood: -4619.757962
EM: Round [995] log likelihood: -4619.757553
EM: Round [996] log likelihood: -4619.757144
EM: Round [997] log likelihood: -4619.756736
EM: Round [998] log likelihood: -4619.756329
EM: Round [999] log likelihood: -4619.755923
EM: Round [1000] log likelihood: -4619.755517
EM: Round [1001] log likelihood: -4619.755112
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295466443
Execution Time = 5.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.DnlGn3U1iD/fi_workdir/microH.dat
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.DnlGn3U1iD/fi_workdir/microH.dat /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/fi_workdir/microH.dat /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.DnlGn3U1iD --json_outfile /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bNS-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.DnlGn3U1iD --json_outfile /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.DnlGn3U1iD/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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir > /tmp/nxf.DnlGn3U1iD/659_bNS-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.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.DnlGn3U1iD/ctat_genome_lib_build_dir > /tmp/nxf.DnlGn3U1iD/659_bNS-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.DnlGn3U1iD/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory