Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/c1cb81e22364bd745fe9a44337fef8/659_ePR-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/e4/d9e4881ec334bebc4adcf0cf238fec/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/d9e4881ec334bebc4adcf0cf238fec/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/0dce45a6f76f92931e401733ee7a67/659_ePR-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/0dce45a6f76f92931e401733ee7a67/659_ePR-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_ePR-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.KRQkfWbPct/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.KRQkfWbPct/cytoBand.txt
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_ePR-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.KRQkfWbPct/fi_workdir --reads "/tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:55:17 ..... started STAR run
Jun 08 09:55:17 ..... loading genome
Jun 08 09:56:58 ... generating Suffix Array index
Jun 08 10:00:44 ... completed Suffix Array index
Jun 08 10:00:45 ..... processing annotations GTF
Jun 08 10:00:45 ..... inserting junctions into the genome indices
Jun 08 10:01:46 ..... started mapping
Jun 08 10:56:59 ..... finished mapping
Jun 08 10:57:00 ..... started sorting BAM
Jun 08 10:57:02 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 61.79 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_ePR-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.KRQkfWbPct/fi_workdir --reads "/tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
10:57:19 : INFO : Done.
Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[2680000]   -done parsing /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 75,
          'low complexity anchor region' => 17,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 16,
          'excessive soft clipping' => 12151,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 99,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 24,
          'per_id < 96' => 9511,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
          'small anchor length' => 212,
          'exons hit < 2' => 9,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 147,
          'seq-similar region overlap' => 442,
          ' ** passed ** ' => 26062,
          'num genes matched < 2' => 15
        };
-writing fusion junction support info.
Execution Time = 1.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[53000]   -fusion SPANNING read extraction for scaff: AC006453.2--GGT2

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[430000]   
[431000]   
[432000]   
[433000]   
[434000]   
[435000]   
[436000]   
[437000]   -fusion SPANNING read extraction for scaff: AC096555.1--PCSK2

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[431000]   
[432000]   
[433000]   
[434000]   
[435000]   
[436000]   
[437000]   
[438000]   
[439000]   -fusion SPANNING read extraction for scaff: ACKR2--PCSK2

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[13000]   
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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   -fusion SPANNING read extraction for scaff: ERBB4--AC093865.1

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: IFT22--ZNF682

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: ME1--AL121977.1

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: ME1--AL121977.2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

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

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

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

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

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

[1000]   
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[6000]   
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[41000]   
[42000]   
[43000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
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[20000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   -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]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[10000]   
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[20000]   
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[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[14000]   
[15000]   
[16000]   
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[18000]   
[19000]   
[20000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

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

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

[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]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

[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]   -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]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

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

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC5

[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]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA11

[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]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHGB3--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGB3--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]   
[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]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[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]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[20000]   
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[100000]   
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[110000]   
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[120000]   
[121000]   
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[130000]   
[131000]   
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[140000]   
[141000]   
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[148000]   
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[150000]   
[151000]   
[152000]   
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[156000]   
[157000]   
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[159000]   
[160000]   
[161000]   
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[170000]   
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[202000]   
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[254000]   
[255000]   
[256000]   
[257000]   
[258000]   
[259000]   
[260000]   
[261000]   -fusion SPANNING read extraction for scaff: TPM3--NTRK1

[1000]   
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[6000]   
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[8000]   
[9000]   
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[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[4000]   
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[6000]   
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[8000]   
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[100000]   
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[472000]   -fusion SPANNING read extraction for scaff: ZNF875--PCSK2
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 92446,
          'lacks exon overlap' => 6275
        };
Execution Time = 3.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -8367.166086
EM: Round [1] log likelihood: -8360.740929
EM: Round [2] log likelihood: -8357.701455
EM: Round [3] log likelihood: -8355.281580
EM: Round [4] log likelihood: -8353.336092
EM: Round [5] log likelihood: -8351.756881
EM: Round [6] log likelihood: -8350.462568
EM: Round [7] log likelihood: -8349.391380
EM: Round [8] log likelihood: -8348.496091
EM: Round [9] log likelihood: -8347.740384
EM: Round [10] log likelihood: -8347.096180
EM: Round [11] log likelihood: -8346.541664
EM: Round [12] log likelihood: -8346.059811
EM: Round [13] log likelihood: -8345.637268
EM: Round [14] log likelihood: -8345.263520
EM: Round [15] log likelihood: -8344.930242
EM: Round [16] log likelihood: -8344.630811
EM: Round [17] log likelihood: -8344.359930
EM: Round [18] log likelihood: -8344.113336
EM: Round [19] log likelihood: -8343.887580
EM: Round [20] log likelihood: -8343.679850
EM: Round [21] log likelihood: -8343.487839
EM: Round [22] log likelihood: -8343.309640
EM: Round [23] log likelihood: -8343.143665
EM: Round [24] log likelihood: -8342.988579
EM: Round [25] log likelihood: -8342.843255
EM: Round [26] log likelihood: -8342.706731
EM: Round [27] log likelihood: -8342.578178
EM: Round [28] log likelihood: -8342.456881
EM: Round [29] log likelihood: -8342.342215
EM: Round [30] log likelihood: -8342.233630
EM: Round [31] log likelihood: -8342.130641
EM: Round [32] log likelihood: -8342.032815
EM: Round [33] log likelihood: -8341.939765
EM: Round [34] log likelihood: -8341.851145
EM: Round [35] log likelihood: -8341.766639
EM: Round [36] log likelihood: -8341.685963
EM: Round [37] log likelihood: -8341.608857
EM: Round [38] log likelihood: -8341.535085
EM: Round [39] log likelihood: -8341.464428
EM: Round [40] log likelihood: -8341.396688
EM: Round [41] log likelihood: -8341.331682
EM: Round [42] log likelihood: -8341.269239
EM: Round [43] log likelihood: -8341.209203
EM: Round [44] log likelihood: -8341.151430
EM: Round [45] log likelihood: -8341.095784
EM: Round [46] log likelihood: -8341.042142
EM: Round [47] log likelihood: -8340.990387
EM: Round [48] log likelihood: -8340.940413
EM: Round [49] log likelihood: -8340.892117
EM: Round [50] log likelihood: -8340.845408
EM: Round [51] log likelihood: -8340.800197
EM: Round [52] log likelihood: -8340.756404
EM: Round [53] log likelihood: -8340.713952
EM: Round [54] log likelihood: -8340.672770
EM: Round [55] log likelihood: -8340.632793
EM: Round [56] log likelihood: -8340.593957
EM: Round [57] log likelihood: -8340.556205
EM: Round [58] log likelihood: -8340.519482
EM: Round [59] log likelihood: -8340.483737
EM: Round [60] log likelihood: -8340.448923
EM: Round [61] log likelihood: -8340.414993
EM: Round [62] log likelihood: -8340.381906
EM: Round [63] log likelihood: -8340.349622
EM: Round [64] log likelihood: -8340.318105
EM: Round [65] log likelihood: -8340.287318
EM: Round [66] log likelihood: -8340.257229
EM: Round [67] log likelihood: -8340.227807
EM: Round [68] log likelihood: -8340.199023
EM: Round [69] log likelihood: -8340.170850
EM: Round [70] log likelihood: -8340.143260
EM: Round [71] log likelihood: -8340.116231
EM: Round [72] log likelihood: -8340.089738
EM: Round [73] log likelihood: -8340.063760
EM: Round [74] log likelihood: -8340.038277
EM: Round [75] log likelihood: -8340.013269
EM: Round [76] log likelihood: -8339.988718
EM: Round [77] log likelihood: -8339.964606
EM: Round [78] log likelihood: -8339.940916
EM: Round [79] log likelihood: -8339.917634
EM: Round [80] log likelihood: -8339.894745
EM: Round [81] log likelihood: -8339.872234
EM: Round [82] log likelihood: -8339.850089
EM: Round [83] log likelihood: -8339.828296
EM: Round [84] log likelihood: -8339.806845
EM: Round [85] log likelihood: -8339.785722
EM: Round [86] log likelihood: -8339.764919
EM: Round [87] log likelihood: -8339.744424
EM: Round [88] log likelihood: -8339.724228
EM: Round [89] log likelihood: -8339.704322
EM: Round [90] log likelihood: -8339.684696
EM: Round [91] log likelihood: -8339.665343
EM: Round [92] log likelihood: -8339.646254
EM: Round [93] log likelihood: -8339.627422
EM: Round [94] log likelihood: -8339.608839
EM: Round [95] log likelihood: -8339.590499
EM: Round [96] log likelihood: -8339.572394
EM: Round [97] log likelihood: -8339.554519
EM: Round [98] log likelihood: -8339.536868
EM: Round [99] log likelihood: -8339.519434
EM: Round [100] log likelihood: -8339.502212
EM: Round [101] log likelihood: -8339.485197
EM: Round [102] log likelihood: -8339.468383
EM: Round [103] log likelihood: -8339.451767
EM: Round [104] log likelihood: -8339.435342
EM: Round [105] log likelihood: -8339.419105
EM: Round [106] log likelihood: -8339.403051
EM: Round [107] log likelihood: -8339.387176
EM: Round [108] log likelihood: -8339.371476
EM: Round [109] log likelihood: -8339.355947
EM: Round [110] log likelihood: -8339.340586
EM: Round [111] log likelihood: -8339.325389
EM: Round [112] log likelihood: -8339.310352
EM: Round [113] log likelihood: -8339.295472
EM: Round [114] log likelihood: -8339.280747
EM: Round [115] log likelihood: -8339.266172
EM: Round [116] log likelihood: -8339.251746
EM: Round [117] log likelihood: -8339.237465
EM: Round [118] log likelihood: -8339.223326
EM: Round [119] log likelihood: -8339.209326
EM: Round [120] log likelihood: -8339.195464
EM: Round [121] log likelihood: -8339.181737
EM: Round [122] log likelihood: -8339.168141
EM: Round [123] log likelihood: -8339.154676
EM: Round [124] log likelihood: -8339.141338
EM: Round [125] log likelihood: -8339.128125
EM: Round [126] log likelihood: -8339.115035
EM: Round [127] log likelihood: -8339.102067
EM: Round [128] log likelihood: -8339.089218
EM: Round [129] log likelihood: -8339.076486
EM: Round [130] log likelihood: -8339.063869
EM: Round [131] log likelihood: -8339.051366
EM: Round [132] log likelihood: -8339.038974
EM: Round [133] log likelihood: -8339.026692
EM: Round [134] log likelihood: -8339.014519
EM: Round [135] log likelihood: -8339.002452
EM: Round [136] log likelihood: -8338.990490
EM: Round [137] log likelihood: -8338.978631
EM: Round [138] log likelihood: -8338.966874
EM: Round [139] log likelihood: -8338.955218
EM: Round [140] log likelihood: -8338.943660
EM: Round [141] log likelihood: -8338.932200
EM: Round [142] log likelihood: -8338.920836
EM: Round [143] log likelihood: -8338.909567
EM: Round [144] log likelihood: -8338.898391
EM: Round [145] log likelihood: -8338.887308
EM: Round [146] log likelihood: -8338.876315
EM: Round [147] log likelihood: -8338.865413
EM: Round [148] log likelihood: -8338.854598
EM: Round [149] log likelihood: -8338.843871
EM: Round [150] log likelihood: -8338.833231
EM: Round [151] log likelihood: -8338.822675
EM: Round [152] log likelihood: -8338.812203
EM: Round [153] log likelihood: -8338.801814
EM: Round [154] log likelihood: -8338.791508
EM: Round [155] log likelihood: -8338.781282
EM: Round [156] log likelihood: -8338.771135
EM: Round [157] log likelihood: -8338.761068
EM: Round [158] log likelihood: -8338.751078
EM: Round [159] log likelihood: -8338.741166
EM: Round [160] log likelihood: -8338.731329
EM: Round [161] log likelihood: -8338.721568
EM: Round [162] log likelihood: -8338.711880
EM: Round [163] log likelihood: -8338.702266
EM: Round [164] log likelihood: -8338.692725
EM: Round [165] log likelihood: -8338.683255
EM: Round [166] log likelihood: -8338.673856
EM: Round [167] log likelihood: -8338.664527
EM: Round [168] log likelihood: -8338.655267
EM: Round [169] log likelihood: -8338.646075
EM: Round [170] log likelihood: -8338.636951
EM: Round [171] log likelihood: -8338.627894
EM: Round [172] log likelihood: -8338.618903
EM: Round [173] log likelihood: -8338.609977
EM: Round [174] log likelihood: -8338.601116
EM: Round [175] log likelihood: -8338.592319
EM: Round [176] log likelihood: -8338.583586
EM: Round [177] log likelihood: -8338.574914
EM: Round [178] log likelihood: -8338.566305
EM: Round [179] log likelihood: -8338.557757
EM: Round [180] log likelihood: -8338.549270
EM: Round [181] log likelihood: -8338.540842
EM: Round [182] log likelihood: -8338.532474
EM: Round [183] log likelihood: -8338.524165
EM: Round [184] log likelihood: -8338.515913
EM: Round [185] log likelihood: -8338.507719
EM: Round [186] log likelihood: -8338.499582
EM: Round [187] log likelihood: -8338.491502
EM: Round [188] log likelihood: -8338.483477
EM: Round [189] log likelihood: -8338.475507
EM: Round [190] log likelihood: -8338.467592
EM: Round [191] log likelihood: -8338.459731
EM: Round [192] log likelihood: -8338.451923
EM: Round [193] log likelihood: -8338.444169
EM: Round [194] log likelihood: -8338.436467
EM: Round [195] log likelihood: -8338.428817
EM: Round [196] log likelihood: -8338.421218
EM: Round [197] log likelihood: -8338.413670
EM: Round [198] log likelihood: -8338.406173
EM: Round [199] log likelihood: -8338.398726
EM: Round [200] log likelihood: -8338.391328
EM: Round [201] log likelihood: -8338.383979
EM: Round [202] log likelihood: -8338.376679
EM: Round [203] log likelihood: -8338.369426
EM: Round [204] log likelihood: -8338.362222
EM: Round [205] log likelihood: -8338.355064
EM: Round [206] log likelihood: -8338.347954
EM: Round [207] log likelihood: -8338.340889
EM: Round [208] log likelihood: -8338.333871
EM: Round [209] log likelihood: -8338.326897
EM: Round [210] log likelihood: -8338.319969
EM: Round [211] log likelihood: -8338.313086
EM: Round [212] log likelihood: -8338.306246
EM: Round [213] log likelihood: -8338.299450
EM: Round [214] log likelihood: -8338.292698
EM: Round [215] log likelihood: -8338.285989
EM: Round [216] log likelihood: -8338.279322
EM: Round [217] log likelihood: -8338.272698
EM: Round [218] log likelihood: -8338.266115
EM: Round [219] log likelihood: -8338.259574
EM: Round [220] log likelihood: -8338.253074
EM: Round [221] log likelihood: -8338.246614
EM: Round [222] log likelihood: -8338.240195
EM: Round [223] log likelihood: -8338.233816
EM: Round [224] log likelihood: -8338.227477
EM: Round [225] log likelihood: -8338.221177
EM: Round [226] log likelihood: -8338.214915
EM: Round [227] log likelihood: -8338.208693
EM: Round [228] log likelihood: -8338.202509
EM: Round [229] log likelihood: -8338.196362
EM: Round [230] log likelihood: -8338.190254
EM: Round [231] log likelihood: -8338.184182
EM: Round [232] log likelihood: -8338.178148
EM: Round [233] log likelihood: -8338.172150
EM: Round [234] log likelihood: -8338.166189
EM: Round [235] log likelihood: -8338.160264
EM: Round [236] log likelihood: -8338.154374
EM: Round [237] log likelihood: -8338.148520
EM: Round [238] log likelihood: -8338.142701
EM: Round [239] log likelihood: -8338.136917
EM: Round [240] log likelihood: -8338.131167
EM: Round [241] log likelihood: -8338.125452
EM: Round [242] log likelihood: -8338.119771
EM: Round [243] log likelihood: -8338.114123
EM: Round [244] log likelihood: -8338.108509
EM: Round [245] log likelihood: -8338.102928
EM: Round [246] log likelihood: -8338.097380
EM: Round [247] log likelihood: -8338.091864
EM: Round [248] log likelihood: -8338.086381
EM: Round [249] log likelihood: -8338.080930
EM: Round [250] log likelihood: -8338.075511
EM: Round [251] log likelihood: -8338.070123
EM: Round [252] log likelihood: -8338.064767
EM: Round [253] log likelihood: -8338.059441
EM: Round [254] log likelihood: -8338.054147
EM: Round [255] log likelihood: -8338.048883
EM: Round [256] log likelihood: -8338.043649
EM: Round [257] log likelihood: -8338.038446
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EM: Round [718] log likelihood: -8337.067228
EM: Round [719] log likelihood: -8337.066477
EM: Round [720] log likelihood: -8337.065728
EM: Round [721] log likelihood: -8337.064982
EM: Round [722] log likelihood: -8337.064238
EM: Round [723] log likelihood: -8337.063496
EM: Round [724] log likelihood: -8337.062757
EM: Round [725] log likelihood: -8337.062021
EM: Round [726] log likelihood: -8337.061286
EM: Round [727] log likelihood: -8337.060555
EM: Round [728] log likelihood: -8337.059825
EM: Round [729] log likelihood: -8337.059098
EM: Round [730] log likelihood: -8337.058373
EM: Round [731] log likelihood: -8337.057651
EM: Round [732] log likelihood: -8337.056931
EM: Round [733] log likelihood: -8337.056213
EM: Round [734] log likelihood: -8337.055498
EM: Round [735] log likelihood: -8337.054785
EM: Round [736] log likelihood: -8337.054074
EM: Round [737] log likelihood: -8337.053366
EM: Round [738] log likelihood: -8337.052660
EM: Round [739] log likelihood: -8337.051956
EM: Round [740] log likelihood: -8337.051255
EM: Round [741] log likelihood: -8337.050556
EM: Round [742] log likelihood: -8337.049859
EM: Round [743] log likelihood: -8337.049164
EM: Round [744] log likelihood: -8337.048471
EM: Round [745] log likelihood: -8337.047781
EM: Round [746] log likelihood: -8337.047093
EM: Round [747] log likelihood: -8337.046407
EM: Round [748] log likelihood: -8337.045724
EM: Round [749] log likelihood: -8337.045042
EM: Round [750] log likelihood: -8337.044363
EM: Round [751] log likelihood: -8337.043686
EM: Round [752] log likelihood: -8337.043011
EM: Round [753] log likelihood: -8337.042339
EM: Round [754] log likelihood: -8337.041668
EM: Round [755] log likelihood: -8337.041000
EM: Round [756] log likelihood: -8337.040334
EM: Round [757] log likelihood: -8337.039670
EM: Round [758] log likelihood: -8337.039008
EM: Round [759] log likelihood: -8337.038348
EM: Round [760] log likelihood: -8337.037690
EM: Round [761] log likelihood: -8337.037034
EM: Round [762] log likelihood: -8337.036381
EM: Round [763] log likelihood: -8337.035729
EM: Round [764] log likelihood: -8337.035080
EM: Round [765] log likelihood: -8337.034433
EM: Round [766] log likelihood: -8337.033788
EM: Round [767] log likelihood: -8337.033144
EM: Round [768] log likelihood: -8337.032503
EM: Round [769] log likelihood: -8337.031864
EM: Round [770] log likelihood: -8337.031227
EM: Round [771] log likelihood: -8337.030592
EM: Round [772] log likelihood: -8337.029959
EM: Round [773] log likelihood: -8337.029328
EM: Round [774] log likelihood: -8337.028699
EM: Round [775] log likelihood: -8337.028072
EM: Round [776] log likelihood: -8337.027447
EM: Round [777] log likelihood: -8337.026824
EM: Round [778] log likelihood: -8337.026203
EM: Round [779] log likelihood: -8337.025584
EM: Round [780] log likelihood: -8337.024966
EM: Round [781] log likelihood: -8337.024351
EM: Round [782] log likelihood: -8337.023738
EM: Round [783] log likelihood: -8337.023126
EM: Round [784] log likelihood: -8337.022517
EM: Round [785] log likelihood: -8337.021909
EM: Round [786] log likelihood: -8337.021304
EM: Round [787] log likelihood: -8337.020700
EM: Round [788] log likelihood: -8337.020098
EM: Round [789] log likelihood: -8337.019498
EM: Round [790] log likelihood: -8337.018900
EM: Round [791] log likelihood: -8337.018304
EM: Round [792] log likelihood: -8337.017710
EM: Round [793] log likelihood: -8337.017117
EM: Round [794] log likelihood: -8337.016527
EM: Round [795] log likelihood: -8337.015938
EM: Round [796] log likelihood: -8337.015351
EM: Round [797] log likelihood: -8337.014766
EM: Round [798] log likelihood: -8337.014183
EM: Round [799] log likelihood: -8337.013602
EM: Round [800] log likelihood: -8337.013022
EM: Round [801] log likelihood: -8337.012444
EM: Round [802] log likelihood: -8337.011868
EM: Round [803] log likelihood: -8337.011294
EM: Round [804] log likelihood: -8337.010722
EM: Round [805] log likelihood: -8337.010151
EM: Round [806] log likelihood: -8337.009582
EM: Round [807] log likelihood: -8337.009015
EM: Round [808] log likelihood: -8337.008450
EM: Round [809] log likelihood: -8337.007886
EM: Round [810] log likelihood: -8337.007324
EM: Round [811] log likelihood: -8337.006764
EM: Round [812] log likelihood: -8337.006206
EM: Round [813] log likelihood: -8337.005649
EM: Round [814] log likelihood: -8337.005094
EM: Round [815] log likelihood: -8337.004541
EM: Round [816] log likelihood: -8337.003990
EM: Round [817] log likelihood: -8337.003440
EM: Round [818] log likelihood: -8337.002892
EM: Round [819] log likelihood: -8337.002345
EM: Round [820] log likelihood: -8337.001801
EM: Round [821] log likelihood: -8337.001258
EM: Round [822] log likelihood: -8337.000716
EM: Round [823] log likelihood: -8337.000177
EM: Round [824] log likelihood: -8336.999639
EM: Round [825] log likelihood: -8336.999102
EM: Round [826] log likelihood: -8336.998567
EM: Round [827] log likelihood: -8336.998034
EM: Round [828] log likelihood: -8336.997503
EM: Round [829] log likelihood: -8336.996973
EM: Round [830] log likelihood: -8336.996445
EM: Round [831] log likelihood: -8336.995918
EM: Round [832] log likelihood: -8336.995393
EM: Round [833] log likelihood: -8336.994870
EM: Round [834] log likelihood: -8336.994348
EM: Round [835] log likelihood: -8336.993828
EM: Round [836] log likelihood: -8336.993310
EM: Round [837] log likelihood: -8336.992793
EM: Round [838] log likelihood: -8336.992277
EM: Round [839] log likelihood: -8336.991763
EM: Round [840] log likelihood: -8336.991251
EM: Round [841] log likelihood: -8336.990740
EM: Round [842] log likelihood: -8336.990231
EM: Round [843] log likelihood: -8336.989724
EM: Round [844] log likelihood: -8336.989217
EM: Round [845] log likelihood: -8336.988713
EM: Round [846] log likelihood: -8336.988210
EM: Round [847] log likelihood: -8336.987709
EM: Round [848] log likelihood: -8336.987209
EM: Round [849] log likelihood: -8336.986710
EM: Round [850] log likelihood: -8336.986213
EM: Round [851] log likelihood: -8336.985718
EM: Round [852] log likelihood: -8336.985224
EM: Round [853] log likelihood: -8336.984732
EM: Round [854] log likelihood: -8336.984241
EM: Round [855] log likelihood: -8336.983751
EM: Round [856] log likelihood: -8336.983263
EM: Round [857] log likelihood: -8336.982777
EM: Round [858] log likelihood: -8336.982292
EM: Round [859] log likelihood: -8336.981808
EM: Round [860] log likelihood: -8336.981326
EM: Round [861] log likelihood: -8336.980845
EM: Round [862] log likelihood: -8336.980366
EM: Round [863] log likelihood: -8336.979888
EM: Round [864] log likelihood: -8336.979412
EM: Round [865] log likelihood: -8336.978937
EM: Round [866] log likelihood: -8336.978464
EM: Round [867] log likelihood: -8336.977992
EM: Round [868] log likelihood: -8336.977521
EM: Round [869] log likelihood: -8336.977052
EM: Round [870] log likelihood: -8336.976584
EM: Round [871] log likelihood: -8336.976118
EM: Round [872] log likelihood: -8336.975653
EM: Round [873] log likelihood: -8336.975189
EM: Round [874] log likelihood: -8336.974727
EM: Round [875] log likelihood: -8336.974266
EM: Round [876] log likelihood: -8336.973807
EM: Round [877] log likelihood: -8336.973349
EM: Round [878] log likelihood: -8336.972892
EM: Round [879] log likelihood: -8336.972437
EM: Round [880] log likelihood: -8336.971983
EM: Round [881] log likelihood: -8336.971530
EM: Round [882] log likelihood: -8336.971079
EM: Round [883] log likelihood: -8336.970629
EM: Round [884] log likelihood: -8336.970180
EM: Round [885] log likelihood: -8336.969733
EM: Round [886] log likelihood: -8336.969287
EM: Round [887] log likelihood: -8336.968842
EM: Round [888] log likelihood: -8336.968399
EM: Round [889] log likelihood: -8336.967957
EM: Round [890] log likelihood: -8336.967517
EM: Round [891] log likelihood: -8336.967077
EM: Round [892] log likelihood: -8336.966639
EM: Round [893] log likelihood: -8336.966203
EM: Round [894] log likelihood: -8336.965767
EM: Round [895] log likelihood: -8336.965333
EM: Round [896] log likelihood: -8336.964900
EM: Round [897] log likelihood: -8336.964468
EM: Round [898] log likelihood: -8336.964038
EM: Round [899] log likelihood: -8336.963609
EM: Round [900] log likelihood: -8336.963181
EM: Round [901] log likelihood: -8336.962755
EM: Round [902] log likelihood: -8336.962330
EM: Round [903] log likelihood: -8336.961906
EM: Round [904] log likelihood: -8336.961483
EM: Round [905] log likelihood: -8336.961061
EM: Round [906] log likelihood: -8336.960641
EM: Round [907] log likelihood: -8336.960222
EM: Round [908] log likelihood: -8336.959804
EM: Round [909] log likelihood: -8336.959388
EM: Round [910] log likelihood: -8336.958973
EM: Round [911] log likelihood: -8336.958558
EM: Round [912] log likelihood: -8336.958146
EM: Round [913] log likelihood: -8336.957734
EM: Round [914] log likelihood: -8336.957323
EM: Round [915] log likelihood: -8336.956914
EM: Round [916] log likelihood: -8336.956506
EM: Round [917] log likelihood: -8336.956099
EM: Round [918] log likelihood: -8336.955694
EM: Round [919] log likelihood: -8336.955289
EM: Round [920] log likelihood: -8336.954886
EM: Round [921] log likelihood: -8336.954484
EM: Round [922] log likelihood: -8336.954083
EM: Round [923] log likelihood: -8336.953683
EM: Round [924] log likelihood: -8336.953284
EM: Round [925] log likelihood: -8336.952887
EM: Round [926] log likelihood: -8336.952491
EM: Round [927] log likelihood: -8336.952095
EM: Round [928] log likelihood: -8336.951702
EM: Round [929] log likelihood: -8336.951309
EM: Round [930] log likelihood: -8336.950917
EM: Round [931] log likelihood: -8336.950526
EM: Round [932] log likelihood: -8336.950137
EM: Round [933] log likelihood: -8336.949749
EM: Round [934] log likelihood: -8336.949362
EM: Round [935] log likelihood: -8336.948976
EM: Round [936] log likelihood: -8336.948591
EM: Round [937] log likelihood: -8336.948207
EM: Round [938] log likelihood: -8336.947824
EM: Round [939] log likelihood: -8336.947443
EM: Round [940] log likelihood: -8336.947062
EM: Round [941] log likelihood: -8336.946683
EM: Round [942] log likelihood: -8336.946305
EM: Round [943] log likelihood: -8336.945928
EM: Round [944] log likelihood: -8336.945552
EM: Round [945] log likelihood: -8336.945177
EM: Round [946] log likelihood: -8336.944803
EM: Round [947] log likelihood: -8336.944430
EM: Round [948] log likelihood: -8336.944058
EM: Round [949] log likelihood: -8336.943688
EM: Round [950] log likelihood: -8336.943318
EM: Round [951] log likelihood: -8336.942950
EM: Round [952] log likelihood: -8336.942582
EM: Round [953] log likelihood: -8336.942216
EM: Round [954] log likelihood: -8336.941850
EM: Round [955] log likelihood: -8336.941486
EM: Round [956] log likelihood: -8336.941123
EM: Round [957] log likelihood: -8336.940761
EM: Round [958] log likelihood: -8336.940400
EM: Round [959] log likelihood: -8336.940039
EM: Round [960] log likelihood: -8336.939680
EM: Round [961] log likelihood: -8336.939322
EM: Round [962] log likelihood: -8336.938965
EM: Round [963] log likelihood: -8336.938609
EM: Round [964] log likelihood: -8336.938254
EM: Round [965] log likelihood: -8336.937900
EM: Round [966] log likelihood: -8336.937548
EM: Round [967] log likelihood: -8336.937196
EM: Round [968] log likelihood: -8336.936845
EM: Round [969] log likelihood: -8336.936495
EM: Round [970] log likelihood: -8336.936146
EM: Round [971] log likelihood: -8336.935798
EM: Round [972] log likelihood: -8336.935451
EM: Round [973] log likelihood: -8336.935105
EM: Round [974] log likelihood: -8336.934760
EM: Round [975] log likelihood: -8336.934416
EM: Round [976] log likelihood: -8336.934073
EM: Round [977] log likelihood: -8336.933731
EM: Round [978] log likelihood: -8336.933390
EM: Round [979] log likelihood: -8336.933050
EM: Round [980] log likelihood: -8336.932711
EM: Round [981] log likelihood: -8336.932373
EM: Round [982] log likelihood: -8336.932036
EM: Round [983] log likelihood: -8336.931700
EM: Round [984] log likelihood: -8336.931365
EM: Round [985] log likelihood: -8336.931030
EM: Round [986] log likelihood: -8336.930697
EM: Round [987] log likelihood: -8336.930365
EM: Round [988] log likelihood: -8336.930033
EM: Round [989] log likelihood: -8336.929703
EM: Round [990] log likelihood: -8336.929373
EM: Round [991] log likelihood: -8336.929045
EM: Round [992] log likelihood: -8336.928717
EM: Round [993] log likelihood: -8336.928390
EM: Round [994] log likelihood: -8336.928064
EM: Round [995] log likelihood: -8336.927740
EM: Round [996] log likelihood: -8336.927416
EM: Round [997] log likelihood: -8336.927092
EM: Round [998] log likelihood: -8336.926770
EM: Round [999] log likelihood: -8336.926449
EM: Round [1000] log likelihood: -8336.926129
EM: Round [1001] log likelihood: -8336.925809
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/fi_workdir/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir
-done, see /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5941.720758
EM: Round [1] log likelihood: -5941.168441
EM: Round [2] log likelihood: -5941.168431
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295913331
Execution Time = 5.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.gtf  > /tmp/nxf.KRQkfWbPct/fi_workdir/microH.dat
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.KRQkfWbPct/fi_workdir/microH.dat /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/fi_workdir/microH.dat /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.KRQkfWbPct --json_outfile /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_ePR-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.KRQkfWbPct --json_outfile /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_ePR-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.KRQkfWbPct/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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_ePR-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_ePR-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir > /tmp/nxf.KRQkfWbPct/659_ePR-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.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000283214.1]
WARNING, no entry stored in dbm for [ENSG00000283214.1]
WARNING, no entry stored in dbm for [ENSG00000283214.1]
WARNING, no entry stored in dbm for [ENSG00000283214.1]
WARNING, no entry stored in dbm for [ENSG00000286152.1]
WARNING, no entry stored in dbm for [ENSG00000273118.1]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.KRQkfWbPct/ctat_genome_lib_build_dir > /tmp/nxf.KRQkfWbPct/659_ePR-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.KRQkfWbPct/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory