Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/67f157d1bfe46a39dc240f6765f082/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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/ca/3ae4b5d4283bf2d1e0d5457238ac4c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/3ae4b5d4283bf2d1e0d5457238ac4c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/a629d2d5fb872373bfa333bb8f2d82/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/a629d2d5fb872373bfa333bb8f2d82/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.gOmQJYduHz/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.gOmQJYduHz/cytoBand.txt
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.gOmQJYduHz/fi_workdir --reads "/tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:26:13 ..... started STAR run
Jun 08 09:26:13 ..... loading genome
Jun 08 09:27:57 ... generating Suffix Array index
Jun 08 09:31:53 ... completed Suffix Array index
Jun 08 09:31:53 ..... processing annotations GTF
Jun 08 09:31:53 ..... inserting junctions into the genome indices
Jun 08 09:32:56 ..... started mapping
Jun 08 10:03:20 ..... finished mapping
Jun 08 10:03:22 ..... started sorting BAM
Jun 08 10:03:22 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 37.18 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.gOmQJYduHz/fi_workdir --reads "/tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
10:03:30 : INFO : Done.
Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

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[1210000]   -done parsing /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'low complexity anchor region' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 13,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'per_id < 96' => 8978,
          'seq-similar region overlap' => 254,
          ' ** passed ** ' => 14272,
          'excessive soft clipping' => 8311,
          'small anchor length' => 160,
          'exons hit < 2' => 3,
          'num genes matched < 2' => 35,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 102,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16
        };
-writing fusion junction support info.
Execution Time = 0.67 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[181000]   -fusion SPANNING read extraction for scaff: CPSF6--DUX4

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[136000]   
[137000]   -fusion SPANNING read extraction for scaff: EPC1--PHC2

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[80000]   
[81000]   -fusion SPANNING read extraction for scaff: FBXO10--SETD2

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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: FXYD1--FXYD5

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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8

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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6

[1000]   
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[5000]   
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[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10

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

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[12000]   
[13000]   
[14000]   
[15000]   
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[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11

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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4

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[17000]   
[18000]   
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[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7

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[34000]   
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[38000]   
[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12

[1000]   
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[30000]   
[31000]   
[32000]   
[33000]   
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[36000]   
[37000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9

[1000]   
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[131000]   
[132000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3

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[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[8000]   
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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[4000]   
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[21000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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

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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[36000]   
[37000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[131000]   
[132000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[20000]   
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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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

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[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[8000]   
[9000]   -fusion SPANNING read extraction for scaff: ZCCHC7--AL513412.1
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 63526,
          'lacks exon overlap' => 1251
        };
Execution Time = 1.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3721.052653
EM: Round [1] log likelihood: -3719.028842
EM: Round [2] log likelihood: -3717.392286
EM: Round [3] log likelihood: -3716.027069
EM: Round [4] log likelihood: -3714.881765
EM: Round [5] log likelihood: -3713.915940
EM: Round [6] log likelihood: -3713.097383
EM: Round [7] log likelihood: -3712.400248
EM: Round [8] log likelihood: -3711.803666
EM: Round [9] log likelihood: -3711.290697
EM: Round [10] log likelihood: -3710.847520
EM: Round [11] log likelihood: -3710.462816
EM: Round [12] log likelihood: -3710.127277
EM: Round [13] log likelihood: -3709.833224
EM: Round [14] log likelihood: -3709.574298
EM: Round [15] log likelihood: -3709.345218
EM: Round [16] log likelihood: -3709.141584
EM: Round [17] log likelihood: -3708.959722
EM: Round [18] log likelihood: -3708.796552
EM: Round [19] log likelihood: -3708.649486
EM: Round [20] log likelihood: -3708.516343
EM: Round [21] log likelihood: -3708.395279
EM: Round [22] log likelihood: -3708.284732
EM: Round [23] log likelihood: -3708.183372
EM: Round [24] log likelihood: -3708.090067
EM: Round [25] log likelihood: -3708.003848
EM: Round [26] log likelihood: -3707.923883
EM: Round [27] log likelihood: -3707.849457
EM: Round [28] log likelihood: -3707.779952
EM: Round [29] log likelihood: -3707.714834
EM: Round [30] log likelihood: -3707.653639
EM: Round [31] log likelihood: -3707.595963
EM: Round [32] log likelihood: -3707.541452
EM: Round [33] log likelihood: -3707.489799
EM: Round [34] log likelihood: -3707.440731
EM: Round [35] log likelihood: -3707.394009
EM: Round [36] log likelihood: -3707.349422
EM: Round [37] log likelihood: -3707.306782
EM: Round [38] log likelihood: -3707.265925
EM: Round [39] log likelihood: -3707.226703
EM: Round [40] log likelihood: -3707.188983
EM: Round [41] log likelihood: -3707.152647
EM: Round [42] log likelihood: -3707.117591
EM: Round [43] log likelihood: -3707.083720
EM: Round [44] log likelihood: -3707.050948
EM: Round [45] log likelihood: -3707.019198
EM: Round [46] log likelihood: -3706.988401
EM: Round [47] log likelihood: -3706.958494
EM: Round [48] log likelihood: -3706.929420
EM: Round [49] log likelihood: -3706.901128
EM: Round [50] log likelihood: -3706.873569
EM: Round [51] log likelihood: -3706.846702
EM: Round [52] log likelihood: -3706.820487
EM: Round [53] log likelihood: -3706.794888
EM: Round [54] log likelihood: -3706.769872
EM: Round [55] log likelihood: -3706.745409
EM: Round [56] log likelihood: -3706.721471
EM: Round [57] log likelihood: -3706.698033
EM: Round [58] log likelihood: -3706.675071
EM: Round [59] log likelihood: -3706.652564
EM: Round [60] log likelihood: -3706.630491
EM: Round [61] log likelihood: -3706.608834
EM: Round [62] log likelihood: -3706.587575
EM: Round [63] log likelihood: -3706.566699
EM: Round [64] log likelihood: -3706.546190
EM: Round [65] log likelihood: -3706.526035
EM: Round [66] log likelihood: -3706.506220
EM: Round [67] log likelihood: -3706.486734
EM: Round [68] log likelihood: -3706.467565
EM: Round [69] log likelihood: -3706.448701
EM: Round [70] log likelihood: -3706.430135
EM: Round [71] log likelihood: -3706.411854
EM: Round [72] log likelihood: -3706.393852
EM: Round [73] log likelihood: -3706.376120
EM: Round [74] log likelihood: -3706.358649
EM: Round [75] log likelihood: -3706.341432
EM: Round [76] log likelihood: -3706.324462
EM: Round [77] log likelihood: -3706.307732
EM: Round [78] log likelihood: -3706.291236
EM: Round [79] log likelihood: -3706.274968
EM: Round [80] log likelihood: -3706.258922
EM: Round [81] log likelihood: -3706.243092
EM: Round [82] log likelihood: -3706.227473
EM: Round [83] log likelihood: -3706.212061
EM: Round [84] log likelihood: -3706.196849
EM: Round [85] log likelihood: -3706.181835
EM: Round [86] log likelihood: -3706.167012
EM: Round [87] log likelihood: -3706.152378
EM: Round [88] log likelihood: -3706.137927
EM: Round [89] log likelihood: -3706.123656
EM: Round [90] log likelihood: -3706.109561
EM: Round [91] log likelihood: -3706.095639
EM: Round [92] log likelihood: -3706.081885
EM: Round [93] log likelihood: -3706.068297
EM: Round [94] log likelihood: -3706.054872
EM: Round [95] log likelihood: -3706.041605
EM: Round [96] log likelihood: -3706.028494
EM: Round [97] log likelihood: -3706.015536
EM: Round [98] log likelihood: -3706.002729
EM: Round [99] log likelihood: -3705.990068
EM: Round [100] log likelihood: -3705.977552
EM: Round [101] log likelihood: -3705.965178
EM: Round [102] log likelihood: -3705.952944
EM: Round [103] log likelihood: -3705.940846
EM: Round [104] log likelihood: -3705.928883
EM: Round [105] log likelihood: -3705.917053
EM: Round [106] log likelihood: -3705.905352
EM: Round [107] log likelihood: -3705.893778
EM: Round [108] log likelihood: -3705.882331
EM: Round [109] log likelihood: -3705.871006
EM: Round [110] log likelihood: -3705.859803
EM: Round [111] log likelihood: -3705.848720
EM: Round [112] log likelihood: -3705.837753
EM: Round [113] log likelihood: -3705.826903
EM: Round [114] log likelihood: -3705.816166
EM: Round [115] log likelihood: -3705.805540
EM: Round [116] log likelihood: -3705.795025
EM: Round [117] log likelihood: -3705.784618
EM: Round [118] log likelihood: -3705.774318
EM: Round [119] log likelihood: -3705.764123
EM: Round [120] log likelihood: -3705.754031
EM: Round [121] log likelihood: -3705.744042
EM: Round [122] log likelihood: -3705.734152
EM: Round [123] log likelihood: -3705.724361
EM: Round [124] log likelihood: -3705.714668
EM: Round [125] log likelihood: -3705.705070
EM: Round [126] log likelihood: -3705.695567
EM: Round [127] log likelihood: -3705.686157
EM: Round [128] log likelihood: -3705.676838
EM: Round [129] log likelihood: -3705.667610
EM: Round [130] log likelihood: -3705.658471
EM: Round [131] log likelihood: -3705.649420
EM: Round [132] log likelihood: -3705.640456
EM: Round [133] log likelihood: -3705.631577
EM: Round [134] log likelihood: -3705.622782
EM: Round [135] log likelihood: -3705.614070
EM: Round [136] log likelihood: -3705.605440
EM: Round [137] log likelihood: -3705.596891
EM: Round [138] log likelihood: -3705.588422
EM: Round [139] log likelihood: -3705.580031
EM: Round [140] log likelihood: -3705.571717
EM: Round [141] log likelihood: -3705.563480
EM: Round [142] log likelihood: -3705.555318
EM: Round [143] log likelihood: -3705.547231
EM: Round [144] log likelihood: -3705.539218
EM: Round [145] log likelihood: -3705.531276
EM: Round [146] log likelihood: -3705.523407
EM: Round [147] log likelihood: -3705.515607
EM: Round [148] log likelihood: -3705.507878
EM: Round [149] log likelihood: -3705.500217
EM: Round [150] log likelihood: -3705.492625
EM: Round [151] log likelihood: -3705.485099
EM: Round [152] log likelihood: -3705.477639
EM: Round [153] log likelihood: -3705.470245
EM: Round [154] log likelihood: -3705.462916
EM: Round [155] log likelihood: -3705.455650
EM: Round [156] log likelihood: -3705.448447
EM: Round [157] log likelihood: -3705.441306
EM: Round [158] log likelihood: -3705.434227
EM: Round [159] log likelihood: -3705.427208
EM: Round [160] log likelihood: -3705.420249
EM: Round [161] log likelihood: -3705.413350
EM: Round [162] log likelihood: -3705.406508
EM: Round [163] log likelihood: -3705.399725
EM: Round [164] log likelihood: -3705.392999
EM: Round [165] log likelihood: -3705.386329
EM: Round [166] log likelihood: -3705.379714
EM: Round [167] log likelihood: -3705.373155
EM: Round [168] log likelihood: -3705.366650
EM: Round [169] log likelihood: -3705.360199
EM: Round [170] log likelihood: -3705.353801
EM: Round [171] log likelihood: -3705.347456
EM: Round [172] log likelihood: -3705.341162
EM: Round [173] log likelihood: -3705.334920
EM: Round [174] log likelihood: -3705.328728
EM: Round [175] log likelihood: -3705.322587
EM: Round [176] log likelihood: -3705.316495
EM: Round [177] log likelihood: -3705.310452
EM: Round [178] log likelihood: -3705.304458
EM: Round [179] log likelihood: -3705.298511
EM: Round [180] log likelihood: -3705.292612
EM: Round [181] log likelihood: -3705.286760
EM: Round [182] log likelihood: -3705.280954
EM: Round [183] log likelihood: -3705.275194
EM: Round [184] log likelihood: -3705.269479
EM: Round [185] log likelihood: -3705.263809
EM: Round [186] log likelihood: -3705.258183
EM: Round [187] log likelihood: -3705.252601
EM: Round [188] log likelihood: -3705.247062
EM: Round [189] log likelihood: -3705.241566
EM: Round [190] log likelihood: -3705.236113
EM: Round [191] log likelihood: -3705.230701
EM: Round [192] log likelihood: -3705.225331
EM: Round [193] log likelihood: -3705.220003
EM: Round [194] log likelihood: -3705.214714
EM: Round [195] log likelihood: -3705.209466
EM: Round [196] log likelihood: -3705.204258
EM: Round [197] log likelihood: -3705.199089
EM: Round [198] log likelihood: -3705.193959
EM: Round [199] log likelihood: -3705.188867
EM: Round [200] log likelihood: -3705.183814
EM: Round [201] log likelihood: -3705.178798
EM: Round [202] log likelihood: -3705.173820
EM: Round [203] log likelihood: -3705.168878
EM: Round [204] log likelihood: -3705.163973
EM: Round [205] log likelihood: -3705.159104
EM: Round [206] log likelihood: -3705.154272
EM: Round [207] log likelihood: -3705.149474
EM: Round [208] log likelihood: -3705.144712
EM: Round [209] log likelihood: -3705.139984
EM: Round [210] log likelihood: -3705.135291
EM: Round [211] log likelihood: -3705.130631
EM: Round [212] log likelihood: -3705.126006
EM: Round [213] log likelihood: -3705.121414
EM: Round [214] log likelihood: -3705.116854
EM: Round [215] log likelihood: -3705.112328
EM: Round [216] log likelihood: -3705.107834
EM: Round [217] log likelihood: -3705.103372
EM: Round [218] log likelihood: -3705.098941
EM: Round [219] log likelihood: -3705.094542
EM: Round [220] log likelihood: -3705.090174
EM: Round [221] log likelihood: -3705.085837
EM: Round [222] log likelihood: -3705.081531
EM: Round [223] log likelihood: -3705.077254
EM: Round [224] log likelihood: -3705.073008
EM: Round [225] log likelihood: -3705.068791
EM: Round [226] log likelihood: -3705.064603
EM: Round [227] log likelihood: -3705.060445
EM: Round [228] log likelihood: -3705.056315
EM: Round [229] log likelihood: -3705.052214
EM: Round [230] log likelihood: -3705.048141
EM: Round [231] log likelihood: -3705.044096
EM: Round [232] log likelihood: -3705.040079
EM: Round [233] log likelihood: -3705.036089
EM: Round [234] log likelihood: -3705.032126
EM: Round [235] log likelihood: -3705.028190
EM: Round [236] log likelihood: -3705.024281
EM: Round [237] log likelihood: -3705.020398
EM: Round [238] log likelihood: -3705.016541
EM: Round [239] log likelihood: -3705.012711
EM: Round [240] log likelihood: -3705.008906
EM: Round [241] log likelihood: -3705.005126
EM: Round [242] log likelihood: -3705.001372
EM: Round [243] log likelihood: -3704.997642
EM: Round [244] log likelihood: -3704.993937
EM: Round [245] log likelihood: -3704.990257
EM: Round [246] log likelihood: -3704.986601
EM: Round [247] log likelihood: -3704.982969
EM: Round [248] log likelihood: -3704.979361
EM: Round [249] log likelihood: -3704.975777
EM: Round [250] log likelihood: -3704.972216
EM: Round [251] log likelihood: -3704.968678
EM: Round [252] log likelihood: -3704.965163
EM: Round [253] log likelihood: -3704.961671
EM: Round [254] log likelihood: -3704.958202
EM: Round [255] log likelihood: -3704.954755
EM: Round [256] log likelihood: -3704.951330
EM: Round [257] log likelihood: -3704.947927
EM: Round [258] log likelihood: -3704.944546
EM: Round [259] log likelihood: -3704.941186
EM: Round [260] log likelihood: -3704.937848
EM: Round [261] log likelihood: -3704.934531
EM: Round [262] log likelihood: -3704.931235
EM: Round [263] log likelihood: -3704.927960
EM: Round [264] log likelihood: -3704.924706
EM: Round [265] log likelihood: -3704.921472
EM: Round [266] log likelihood: -3704.918258
EM: Round [267] log likelihood: -3704.915065
EM: Round [268] log likelihood: -3704.911891
EM: Round [269] log likelihood: -3704.908737
EM: Round [270] log likelihood: -3704.905603
EM: Round [271] log likelihood: -3704.902488
EM: Round [272] log likelihood: -3704.899393
EM: Round [273] log likelihood: -3704.896316
EM: Round [274] log likelihood: -3704.893258
EM: Round [275] log likelihood: -3704.890220
EM: Round [276] log likelihood: -3704.887200
EM: Round [277] log likelihood: -3704.884198
EM: Round [278] log likelihood: -3704.881214
EM: Round [279] log likelihood: -3704.878249
EM: Round [280] log likelihood: -3704.875302
EM: Round [281] log likelihood: -3704.872372
EM: Round [282] log likelihood: -3704.869460
EM: Round [283] log likelihood: -3704.866566
EM: Round [284] log likelihood: -3704.863689
EM: Round [285] log likelihood: -3704.860829
EM: Round [286] log likelihood: -3704.857987
EM: Round [287] log likelihood: -3704.855161
EM: Round [288] log likelihood: -3704.852352
EM: Round [289] log likelihood: -3704.849560
EM: Round [290] log likelihood: -3704.846784
EM: Round [291] log likelihood: -3704.844025
EM: Round [292] log likelihood: -3704.841282
EM: Round [293] log likelihood: -3704.838555
EM: Round [294] log likelihood: -3704.835844
EM: Round [295] log likelihood: -3704.833149
EM: Round [296] log likelihood: -3704.830470
EM: Round [297] log likelihood: -3704.827806
EM: Round [298] log likelihood: -3704.825158
EM: Round [299] log likelihood: -3704.822525
EM: Round [300] log likelihood: -3704.819908
EM: Round [301] log likelihood: -3704.817305
EM: Round [302] log likelihood: -3704.814717
EM: Round [303] log likelihood: -3704.812145
EM: Round [304] log likelihood: -3704.809587
EM: Round [305] log likelihood: -3704.807043
EM: Round [306] log likelihood: -3704.804514
EM: Round [307] log likelihood: -3704.802000
EM: Round [308] log likelihood: -3704.799499
EM: Round [309] log likelihood: -3704.797013
EM: Round [310] log likelihood: -3704.794541
EM: Round [311] log likelihood: -3704.792083
EM: Round [312] log likelihood: -3704.789639
EM: Round [313] log likelihood: -3704.787208
EM: Round [314] log likelihood: -3704.784791
EM: Round [315] log likelihood: -3704.782388
EM: Round [316] log likelihood: -3704.779997
EM: Round [317] log likelihood: -3704.777621
EM: Round [318] log likelihood: -3704.775257
EM: Round [319] log likelihood: -3704.772906
EM: Round [320] log likelihood: -3704.770569
EM: Round [321] log likelihood: -3704.768244
EM: Round [322] log likelihood: -3704.765932
EM: Round [323] log likelihood: -3704.763632
EM: Round [324] log likelihood: -3704.761346
EM: Round [325] log likelihood: -3704.759071
EM: Round [326] log likelihood: -3704.756809
EM: Round [327] log likelihood: -3704.754560
EM: Round [328] log likelihood: -3704.752322
EM: Round [329] log likelihood: -3704.750097
EM: Round [330] log likelihood: -3704.747884
EM: Round [331] log likelihood: -3704.745682
EM: Round [332] log likelihood: -3704.743492
EM: Round [333] log likelihood: -3704.741315
EM: Round [334] log likelihood: -3704.739148
EM: Round [335] log likelihood: -3704.736994
EM: Round [336] log likelihood: -3704.734850
EM: Round [337] log likelihood: -3704.732718
EM: Round [338] log likelihood: -3704.730598
EM: Round [339] log likelihood: -3704.728488
EM: Round [340] log likelihood: -3704.726390
EM: Round [341] log likelihood: -3704.724303
EM: Round [342] log likelihood: -3704.722227
EM: Round [343] log likelihood: -3704.720161
EM: Round [344] log likelihood: -3704.718107
EM: Round [345] log likelihood: -3704.716063
EM: Round [346] log likelihood: -3704.714029
EM: Round [347] log likelihood: -3704.712007
EM: Round [348] log likelihood: -3704.709994
EM: Round [349] log likelihood: -3704.707992
EM: Round [350] log likelihood: -3704.706001
EM: Round [351] log likelihood: -3704.704020
EM: Round [352] log likelihood: -3704.702048
EM: Round [353] log likelihood: -3704.700087
EM: Round [354] log likelihood: -3704.698136
EM: Round [355] log likelihood: -3704.696195
EM: Round [356] log likelihood: -3704.694264
EM: Round [357] log likelihood: -3704.692343
EM: Round [358] log likelihood: -3704.690431
EM: Round [359] log likelihood: -3704.688529
EM: Round [360] log likelihood: -3704.686637
EM: Round [361] log likelihood: -3704.684754
EM: Round [362] log likelihood: -3704.682880
EM: Round [363] log likelihood: -3704.681016
EM: Round [364] log likelihood: -3704.679161
EM: Round [365] log likelihood: -3704.677316
EM: Round [366] log likelihood: -3704.675480
EM: Round [367] log likelihood: -3704.673652
EM: Round [368] log likelihood: -3704.671834
EM: Round [369] log likelihood: -3704.670025
EM: Round [370] log likelihood: -3704.668225
EM: Round [371] log likelihood: -3704.666433
EM: Round [372] log likelihood: -3704.664651
EM: Round [373] log likelihood: -3704.662877
EM: Round [374] log likelihood: -3704.661112
EM: Round [375] log likelihood: -3704.659355
EM: Round [376] log likelihood: -3704.657607
EM: Round [377] log likelihood: -3704.655868
EM: Round [378] log likelihood: -3704.654137
EM: Round [379] log likelihood: -3704.652414
EM: Round [380] log likelihood: -3704.650699
EM: Round [381] log likelihood: -3704.648993
EM: Round [382] log likelihood: -3704.647295
EM: Round [383] log likelihood: -3704.645605
EM: Round [384] log likelihood: -3704.643924
EM: Round [385] log likelihood: -3704.642250
EM: Round [386] log likelihood: -3704.640584
EM: Round [387] log likelihood: -3704.638926
EM: Round [388] log likelihood: -3704.637277
EM: Round [389] log likelihood: -3704.635634
EM: Round [390] log likelihood: -3704.634000
EM: Round [391] log likelihood: -3704.632373
EM: Round [392] log likelihood: -3704.630754
EM: Round [393] log likelihood: -3704.629143
EM: Round [394] log likelihood: -3704.627539
EM: Round [395] log likelihood: -3704.625943
EM: Round [396] log likelihood: -3704.624354
EM: Round [397] log likelihood: -3704.622772
EM: Round [398] log likelihood: -3704.621198
EM: Round [399] log likelihood: -3704.619631
EM: Round [400] log likelihood: -3704.618071
EM: Round [401] log likelihood: -3704.616519
EM: Round [402] log likelihood: -3704.614974
EM: Round [403] log likelihood: -3704.613435
EM: Round [404] log likelihood: -3704.611904
EM: Round [405] log likelihood: -3704.610380
EM: Round [406] log likelihood: -3704.608863
EM: Round [407] log likelihood: -3704.607353
EM: Round [408] log likelihood: -3704.605849
EM: Round [409] log likelihood: -3704.604353
EM: Round [410] log likelihood: -3704.602863
EM: Round [411] log likelihood: -3704.601380
EM: Round [412] log likelihood: -3704.599903
EM: Round [413] log likelihood: -3704.598434
EM: Round [414] log likelihood: -3704.596971
EM: Round [415] log likelihood: -3704.595514
EM: Round [416] log likelihood: -3704.594064
EM: Round [417] log likelihood: -3704.592620
EM: Round [418] log likelihood: -3704.591183
EM: Round [419] log likelihood: -3704.589752
EM: Round [420] log likelihood: -3704.588328
EM: Round [421] log likelihood: -3704.586910
EM: Round [422] log likelihood: -3704.585498
EM: Round [423] log likelihood: -3704.584092
EM: Round [424] log likelihood: -3704.582693
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EM: Round [882] log likelihood: -3704.268281
EM: Round [883] log likelihood: -3704.267957
EM: Round [884] log likelihood: -3704.267634
EM: Round [885] log likelihood: -3704.267312
EM: Round [886] log likelihood: -3704.266991
EM: Round [887] log likelihood: -3704.266670
EM: Round [888] log likelihood: -3704.266351
EM: Round [889] log likelihood: -3704.266032
EM: Round [890] log likelihood: -3704.265714
EM: Round [891] log likelihood: -3704.265397
EM: Round [892] log likelihood: -3704.265080
EM: Round [893] log likelihood: -3704.264765
EM: Round [894] log likelihood: -3704.264450
EM: Round [895] log likelihood: -3704.264136
EM: Round [896] log likelihood: -3704.263823
EM: Round [897] log likelihood: -3704.263511
EM: Round [898] log likelihood: -3704.263199
EM: Round [899] log likelihood: -3704.262888
EM: Round [900] log likelihood: -3704.262578
EM: Round [901] log likelihood: -3704.262269
EM: Round [902] log likelihood: -3704.261961
EM: Round [903] log likelihood: -3704.261653
EM: Round [904] log likelihood: -3704.261346
EM: Round [905] log likelihood: -3704.261040
EM: Round [906] log likelihood: -3704.260735
EM: Round [907] log likelihood: -3704.260430
EM: Round [908] log likelihood: -3704.260126
EM: Round [909] log likelihood: -3704.259823
EM: Round [910] log likelihood: -3704.259521
EM: Round [911] log likelihood: -3704.259219
EM: Round [912] log likelihood: -3704.258919
EM: Round [913] log likelihood: -3704.258619
EM: Round [914] log likelihood: -3704.258319
EM: Round [915] log likelihood: -3704.258021
EM: Round [916] log likelihood: -3704.257723
EM: Round [917] log likelihood: -3704.257426
EM: Round [918] log likelihood: -3704.257130
EM: Round [919] log likelihood: -3704.256834
EM: Round [920] log likelihood: -3704.256540
EM: Round [921] log likelihood: -3704.256246
EM: Round [922] log likelihood: -3704.255952
EM: Round [923] log likelihood: -3704.255660
EM: Round [924] log likelihood: -3704.255368
EM: Round [925] log likelihood: -3704.255077
EM: Round [926] log likelihood: -3704.254786
EM: Round [927] log likelihood: -3704.254497
EM: Round [928] log likelihood: -3704.254208
EM: Round [929] log likelihood: -3704.253920
EM: Round [930] log likelihood: -3704.253632
EM: Round [931] log likelihood: -3704.253345
EM: Round [932] log likelihood: -3704.253059
EM: Round [933] log likelihood: -3704.252774
EM: Round [934] log likelihood: -3704.252489
EM: Round [935] log likelihood: -3704.252205
EM: Round [936] log likelihood: -3704.251922
EM: Round [937] log likelihood: -3704.251640
EM: Round [938] log likelihood: -3704.251358
EM: Round [939] log likelihood: -3704.251077
EM: Round [940] log likelihood: -3704.250796
EM: Round [941] log likelihood: -3704.250517
EM: Round [942] log likelihood: -3704.250238
EM: Round [943] log likelihood: -3704.249959
EM: Round [944] log likelihood: -3704.249682
EM: Round [945] log likelihood: -3704.249405
EM: Round [946] log likelihood: -3704.249128
EM: Round [947] log likelihood: -3704.248853
EM: Round [948] log likelihood: -3704.248578
EM: Round [949] log likelihood: -3704.248304
EM: Round [950] log likelihood: -3704.248030
EM: Round [951] log likelihood: -3704.247757
EM: Round [952] log likelihood: -3704.247485
EM: Round [953] log likelihood: -3704.247214
EM: Round [954] log likelihood: -3704.246943
EM: Round [955] log likelihood: -3704.246673
EM: Round [956] log likelihood: -3704.246403
EM: Round [957] log likelihood: -3704.246134
EM: Round [958] log likelihood: -3704.245866
EM: Round [959] log likelihood: -3704.245598
EM: Round [960] log likelihood: -3704.245332
EM: Round [961] log likelihood: -3704.245065
EM: Round [962] log likelihood: -3704.244800
EM: Round [963] log likelihood: -3704.244535
EM: Round [964] log likelihood: -3704.244271
EM: Round [965] log likelihood: -3704.244007
EM: Round [966] log likelihood: -3704.243744
EM: Round [967] log likelihood: -3704.243482
EM: Round [968] log likelihood: -3704.243220
EM: Round [969] log likelihood: -3704.242959
EM: Round [970] log likelihood: -3704.242699
EM: Round [971] log likelihood: -3704.242439
EM: Round [972] log likelihood: -3704.242180
EM: Round [973] log likelihood: -3704.241922
EM: Round [974] log likelihood: -3704.241664
EM: Round [975] log likelihood: -3704.241407
EM: Round [976] log likelihood: -3704.241150
EM: Round [977] log likelihood: -3704.240894
EM: Round [978] log likelihood: -3704.240639
EM: Round [979] log likelihood: -3704.240384
EM: Round [980] log likelihood: -3704.240130
EM: Round [981] log likelihood: -3704.239877
EM: Round [982] log likelihood: -3704.239624
EM: Round [983] log likelihood: -3704.239372
EM: Round [984] log likelihood: -3704.239120
EM: Round [985] log likelihood: -3704.238869
EM: Round [986] log likelihood: -3704.238619
EM: Round [987] log likelihood: -3704.238369
EM: Round [988] log likelihood: -3704.238120
EM: Round [989] log likelihood: -3704.237871
EM: Round [990] log likelihood: -3704.237623
EM: Round [991] log likelihood: -3704.237376
EM: Round [992] log likelihood: -3704.237129
EM: Round [993] log likelihood: -3704.236883
EM: Round [994] log likelihood: -3704.236638
EM: Round [995] log likelihood: -3704.236393
EM: Round [996] log likelihood: -3704.236149
EM: Round [997] log likelihood: -3704.235905
EM: Round [998] log likelihood: -3704.235662
EM: Round [999] log likelihood: -3704.235419
EM: Round [1000] log likelihood: -3704.235177
EM: Round [1001] log likelihood: -3704.234936
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir
-done, see /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -3418.842870
EM: Round [1] log likelihood: -3418.792022
EM: Round [2] log likelihood: -3418.791798
EM: Round [3] log likelihood: -3418.791796
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 146712425
Execution Time = 2.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.gOmQJYduHz/fi_workdir/microH.dat
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.gOmQJYduHz/fi_workdir/microH.dat /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/fi_workdir/microH.dat /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.gOmQJYduHz --json_outfile /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.gOmQJYduHz --json_outfile /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.gOmQJYduHz/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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_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.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
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 [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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.gOmQJYduHz/ctat_genome_lib_build_dir > /tmp/nxf.gOmQJYduHz/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.gOmQJYduHz/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory