Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/8957d06de4532201e4792f62794a16/1173_Q7O_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/33/93e7e0466d38633801634d24a104cd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/93e7e0466d38633801634d24a104cd/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/a0bab5da9a1d55b9d818b62d05a483/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/a0bab5da9a1d55b9d818b62d05a483/1173_Q7O_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_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_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 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4edL9IDkmh/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4edL9IDkmh/cytoBand.txt
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed
-parsing GTF file: /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.4edL9IDkmh/fi_workdir --reads "/tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 11:18:45 ..... started STAR run
Jun 08 11:18:45 ..... loading genome
Jun 08 11:20:26 ... generating Suffix Array index
Jun 08 11:24:16 ... completed Suffix Array index
Jun 08 11:24:16 ..... processing annotations GTF
Jun 08 11:24:16 ..... inserting junctions into the genome indices
Jun 08 11:25:17 ..... started mapping
Jun 08 12:09:19 ..... finished mapping
Jun 08 12:09:20 ..... started sorting BAM
Jun 08 12:09:21 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
Execution Time = 50.63 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.4edL9IDkmh/fi_workdir --reads "/tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
12:09:34 : INFO : Done.
Execution Time = 0.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

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[2360000]   -done parsing /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 94,
          'excessive soft clipping' => 14054,
          'low complexity anchor region' => 13,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 910,
          'seq-similar region overlap' => 977,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 6,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1454,
          'small anchor length' => 124,
          'num genes matched < 2' => 43,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 21,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 417,
          ' ** passed ** ' => 18503,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 140,
          'per_id < 96' => 27796
        };
-writing fusion junction support info.
Execution Time = 1.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[12000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[640000]   
[641000]   -fusion SPANNING read extraction for scaff: MEOX2--CRPPA

[1000]   
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[8000]   
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[64000]   
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[66000]   
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[69000]   
[70000]   
[71000]   
[72000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: OR8D1--OR8A1

[1000]   
[2000]   
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[6000]   
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[134000]   
[135000]   
[136000]   
[137000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[153000]   
[154000]   
[155000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
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[8000]   
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[135000]   
[136000]   
[137000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
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[96000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[113000]   
[114000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[95000]   
[96000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[46000]   
[47000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[33000]   
[34000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
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[25000]   
[26000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
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[30000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[31000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[38000]   
[39000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[1000]   
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[173000]   
[174000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[21000]   -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146

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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: SLC5A4P1--OR8A1

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[123000]   
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[127000]   
[128000]   
[129000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[55000]   
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[60000]   
[61000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[20000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
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[16000]   
[17000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[77000]   
[78000]   -fusion SPANNING read extraction for scaff: WASH3P--LINC01237

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[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   -fusion SPANNING read extraction for scaff: WASH3P--LINC01880
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 6695,
          'seq similar region alignment' => 101873
        };
Execution Time = 2.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7273.703393
EM: Round [1] log likelihood: -7273.257842
EM: Round [2] log likelihood: -7272.947475
EM: Round [3] log likelihood: -7272.654027
EM: Round [4] log likelihood: -7272.376074
EM: Round [5] log likelihood: -7272.112452
EM: Round [6] log likelihood: -7271.862109
EM: Round [7] log likelihood: -7271.624091
EM: Round [8] log likelihood: -7271.397534
EM: Round [9] log likelihood: -7271.181649
EM: Round [10] log likelihood: -7270.975720
EM: Round [11] log likelihood: -7270.779091
EM: Round [12] log likelihood: -7270.591163
EM: Round [13] log likelihood: -7270.411388
EM: Round [14] log likelihood: -7270.239265
EM: Round [15] log likelihood: -7270.074332
EM: Round [16] log likelihood: -7269.916167
EM: Round [17] log likelihood: -7269.764378
EM: Round [18] log likelihood: -7269.618608
EM: Round [19] log likelihood: -7269.478524
EM: Round [20] log likelihood: -7269.343821
EM: Round [21] log likelihood: -7269.214214
EM: Round [22] log likelihood: -7269.089442
EM: Round [23] log likelihood: -7268.969260
EM: Round [24] log likelihood: -7268.853442
EM: Round [25] log likelihood: -7268.741776
EM: Round [26] log likelihood: -7268.634066
EM: Round [27] log likelihood: -7268.530128
EM: Round [28] log likelihood: -7268.429789
EM: Round [29] log likelihood: -7268.332890
EM: Round [30] log likelihood: -7268.239277
EM: Round [31] log likelihood: -7268.148810
EM: Round [32] log likelihood: -7268.061354
EM: Round [33] log likelihood: -7267.976783
EM: Round [34] log likelihood: -7267.894979
EM: Round [35] log likelihood: -7267.815827
EM: Round [36] log likelihood: -7267.739222
EM: Round [37] log likelihood: -7267.665062
EM: Round [38] log likelihood: -7267.593251
EM: Round [39] log likelihood: -7267.523698
EM: Round [40] log likelihood: -7267.456315
EM: Round [41] log likelihood: -7267.391021
EM: Round [42] log likelihood: -7267.327734
EM: Round [43] log likelihood: -7267.266381
EM: Round [44] log likelihood: -7267.206889
EM: Round [45] log likelihood: -7267.149189
EM: Round [46] log likelihood: -7267.093214
EM: Round [47] log likelihood: -7267.038902
EM: Round [48] log likelihood: -7266.986191
EM: Round [49] log likelihood: -7266.935024
EM: Round [50] log likelihood: -7266.885344
EM: Round [51] log likelihood: -7266.837097
EM: Round [52] log likelihood: -7266.790233
EM: Round [53] log likelihood: -7266.744700
EM: Round [54] log likelihood: -7266.700453
EM: Round [55] log likelihood: -7266.657443
EM: Round [56] log likelihood: -7266.615629
EM: Round [57] log likelihood: -7266.574966
EM: Round [58] log likelihood: -7266.535414
EM: Round [59] log likelihood: -7266.496934
EM: Round [60] log likelihood: -7266.459487
EM: Round [61] log likelihood: -7266.423038
EM: Round [62] log likelihood: -7266.387550
EM: Round [63] log likelihood: -7266.352990
EM: Round [64] log likelihood: -7266.319325
EM: Round [65] log likelihood: -7266.286524
EM: Round [66] log likelihood: -7266.254556
EM: Round [67] log likelihood: -7266.223393
EM: Round [68] log likelihood: -7266.193005
EM: Round [69] log likelihood: -7266.163366
EM: Round [70] log likelihood: -7266.134450
EM: Round [71] log likelihood: -7266.106231
EM: Round [72] log likelihood: -7266.078686
EM: Round [73] log likelihood: -7266.051790
EM: Round [74] log likelihood: -7266.025522
EM: Round [75] log likelihood: -7265.999859
EM: Round [76] log likelihood: -7265.974781
EM: Round [77] log likelihood: -7265.950268
EM: Round [78] log likelihood: -7265.926299
EM: Round [79] log likelihood: -7265.902857
EM: Round [80] log likelihood: -7265.879924
EM: Round [81] log likelihood: -7265.857482
EM: Round [82] log likelihood: -7265.835514
EM: Round [83] log likelihood: -7265.814005
EM: Round [84] log likelihood: -7265.792939
EM: Round [85] log likelihood: -7265.772301
EM: Round [86] log likelihood: -7265.752076
EM: Round [87] log likelihood: -7265.732252
EM: Round [88] log likelihood: -7265.712814
EM: Round [89] log likelihood: -7265.693750
EM: Round [90] log likelihood: -7265.675047
EM: Round [91] log likelihood: -7265.656695
EM: Round [92] log likelihood: -7265.638680
EM: Round [93] log likelihood: -7265.620993
EM: Round [94] log likelihood: -7265.603623
EM: Round [95] log likelihood: -7265.586559
EM: Round [96] log likelihood: -7265.569793
EM: Round [97] log likelihood: -7265.553313
EM: Round [98] log likelihood: -7265.537112
EM: Round [99] log likelihood: -7265.521180
EM: Round [100] log likelihood: -7265.505510
EM: Round [101] log likelihood: -7265.490093
EM: Round [102] log likelihood: -7265.474921
EM: Round [103] log likelihood: -7265.459987
EM: Round [104] log likelihood: -7265.445283
EM: Round [105] log likelihood: -7265.430803
EM: Round [106] log likelihood: -7265.416541
EM: Round [107] log likelihood: -7265.402489
EM: Round [108] log likelihood: -7265.388641
EM: Round [109] log likelihood: -7265.374992
EM: Round [110] log likelihood: -7265.361536
EM: Round [111] log likelihood: -7265.348266
EM: Round [112] log likelihood: -7265.335179
EM: Round [113] log likelihood: -7265.322269
EM: Round [114] log likelihood: -7265.309530
EM: Round [115] log likelihood: -7265.296959
EM: Round [116] log likelihood: -7265.284550
EM: Round [117] log likelihood: -7265.272299
EM: Round [118] log likelihood: -7265.260202
EM: Round [119] log likelihood: -7265.248255
EM: Round [120] log likelihood: -7265.236454
EM: Round [121] log likelihood: -7265.224795
EM: Round [122] log likelihood: -7265.213275
EM: Round [123] log likelihood: -7265.201890
EM: Round [124] log likelihood: -7265.190636
EM: Round [125] log likelihood: -7265.179510
EM: Round [126] log likelihood: -7265.168510
EM: Round [127] log likelihood: -7265.157631
EM: Round [128] log likelihood: -7265.146872
EM: Round [129] log likelihood: -7265.136229
EM: Round [130] log likelihood: -7265.125700
EM: Round [131] log likelihood: -7265.115281
EM: Round [132] log likelihood: -7265.104971
EM: Round [133] log likelihood: -7265.094767
EM: Round [134] log likelihood: -7265.084667
EM: Round [135] log likelihood: -7265.074668
EM: Round [136] log likelihood: -7265.064768
EM: Round [137] log likelihood: -7265.054965
EM: Round [138] log likelihood: -7265.045257
EM: Round [139] log likelihood: -7265.035642
EM: Round [140] log likelihood: -7265.026118
EM: Round [141] log likelihood: -7265.016683
EM: Round [142] log likelihood: -7265.007335
EM: Round [143] log likelihood: -7264.998073
EM: Round [144] log likelihood: -7264.988895
EM: Round [145] log likelihood: -7264.979799
EM: Round [146] log likelihood: -7264.970784
EM: Round [147] log likelihood: -7264.961848
EM: Round [148] log likelihood: -7264.952990
EM: Round [149] log likelihood: -7264.944208
EM: Round [150] log likelihood: -7264.935501
EM: Round [151] log likelihood: -7264.926867
EM: Round [152] log likelihood: -7264.918306
EM: Round [153] log likelihood: -7264.909816
EM: Round [154] log likelihood: -7264.901395
EM: Round [155] log likelihood: -7264.893043
EM: Round [156] log likelihood: -7264.884758
EM: Round [157] log likelihood: -7264.876540
EM: Round [158] log likelihood: -7264.868387
EM: Round [159] log likelihood: -7264.860298
EM: Round [160] log likelihood: -7264.852272
EM: Round [161] log likelihood: -7264.844309
EM: Round [162] log likelihood: -7264.836406
EM: Round [163] log likelihood: -7264.828564
EM: Round [164] log likelihood: -7264.820781
EM: Round [165] log likelihood: -7264.813056
EM: Round [166] log likelihood: -7264.805390
EM: Round [167] log likelihood: -7264.797779
EM: Round [168] log likelihood: -7264.790225
EM: Round [169] log likelihood: -7264.782726
EM: Round [170] log likelihood: -7264.775281
EM: Round [171] log likelihood: -7264.767890
EM: Round [172] log likelihood: -7264.760551
EM: Round [173] log likelihood: -7264.753265
EM: Round [174] log likelihood: -7264.746030
EM: Round [175] log likelihood: -7264.738846
EM: Round [176] log likelihood: -7264.731712
EM: Round [177] log likelihood: -7264.724628
EM: Round [178] log likelihood: -7264.717592
EM: Round [179] log likelihood: -7264.710604
EM: Round [180] log likelihood: -7264.703664
EM: Round [181] log likelihood: -7264.696771
EM: Round [182] log likelihood: -7264.689924
EM: Round [183] log likelihood: -7264.683124
EM: Round [184] log likelihood: -7264.676368
EM: Round [185] log likelihood: -7264.669657
EM: Round [186] log likelihood: -7264.662991
EM: Round [187] log likelihood: -7264.656368
EM: Round [188] log likelihood: -7264.649788
EM: Round [189] log likelihood: -7264.643251
EM: Round [190] log likelihood: -7264.636756
EM: Round [191] log likelihood: -7264.630303
EM: Round [192] log likelihood: -7264.623891
EM: Round [193] log likelihood: -7264.617520
EM: Round [194] log likelihood: -7264.611190
EM: Round [195] log likelihood: -7264.604899
EM: Round [196] log likelihood: -7264.598648
EM: Round [197] log likelihood: -7264.592436
EM: Round [198] log likelihood: -7264.586263
EM: Round [199] log likelihood: -7264.580127
EM: Round [200] log likelihood: -7264.574030
EM: Round [201] log likelihood: -7264.567970
EM: Round [202] log likelihood: -7264.561948
EM: Round [203] log likelihood: -7264.555962
EM: Round [204] log likelihood: -7264.550012
EM: Round [205] log likelihood: -7264.544099
EM: Round [206] log likelihood: -7264.538221
EM: Round [207] log likelihood: -7264.532378
EM: Round [208] log likelihood: -7264.526570
EM: Round [209] log likelihood: -7264.520797
EM: Round [210] log likelihood: -7264.515059
EM: Round [211] log likelihood: -7264.509354
EM: Round [212] log likelihood: -7264.503682
EM: Round [213] log likelihood: -7264.498044
EM: Round [214] log likelihood: -7264.492439
EM: Round [215] log likelihood: -7264.486867
EM: Round [216] log likelihood: -7264.481327
EM: Round [217] log likelihood: -7264.475820
EM: Round [218] log likelihood: -7264.470344
EM: Round [219] log likelihood: -7264.464899
EM: Round [220] log likelihood: -7264.459486
EM: Round [221] log likelihood: -7264.454104
EM: Round [222] log likelihood: -7264.448752
EM: Round [223] log likelihood: -7264.443431
EM: Round [224] log likelihood: -7264.438140
EM: Round [225] log likelihood: -7264.432878
EM: Round [226] log likelihood: -7264.427647
EM: Round [227] log likelihood: -7264.422445
EM: Round [228] log likelihood: -7264.417271
EM: Round [229] log likelihood: -7264.412127
EM: Round [230] log likelihood: -7264.407012
EM: Round [231] log likelihood: -7264.401924
EM: Round [232] log likelihood: -7264.396865
EM: Round [233] log likelihood: -7264.391834
EM: Round [234] log likelihood: -7264.386830
EM: Round [235] log likelihood: -7264.381854
EM: Round [236] log likelihood: -7264.376905
EM: Round [237] log likelihood: -7264.371983
EM: Round [238] log likelihood: -7264.367088
EM: Round [239] log likelihood: -7264.362219
EM: Round [240] log likelihood: -7264.357377
EM: Round [241] log likelihood: -7264.352560
EM: Round [242] log likelihood: -7264.347770
EM: Round [243] log likelihood: -7264.343006
EM: Round [244] log likelihood: -7264.338266
EM: Round [245] log likelihood: -7264.333553
EM: Round [246] log likelihood: -7264.328864
EM: Round [247] log likelihood: -7264.324200
EM: Round [248] log likelihood: -7264.319561
EM: Round [249] log likelihood: -7264.314946
EM: Round [250] log likelihood: -7264.310356
EM: Round [251] log likelihood: -7264.305790
EM: Round [252] log likelihood: -7264.301248
EM: Round [253] log likelihood: -7264.296729
EM: Round [254] log likelihood: -7264.292234
EM: Round [255] log likelihood: -7264.287763
EM: Round [256] log likelihood: -7264.283315
EM: Round [257] log likelihood: -7264.278890
EM: Round [258] log likelihood: -7264.274487
EM: Round [259] log likelihood: -7264.270108
EM: Round [260] log likelihood: -7264.265751
EM: Round [261] log likelihood: -7264.261416
EM: Round [262] log likelihood: -7264.257104
EM: Round [263] log likelihood: -7264.252814
EM: Round [264] log likelihood: -7264.248545
EM: Round [265] log likelihood: -7264.244298
EM: Round [266] log likelihood: -7264.240073
EM: Round [267] log likelihood: -7264.235869
EM: Round [268] log likelihood: -7264.231687
EM: Round [269] log likelihood: -7264.227525
EM: Round [270] log likelihood: -7264.223385
EM: Round [271] log likelihood: -7264.219265
EM: Round [272] log likelihood: -7264.215166
EM: Round [273] log likelihood: -7264.211088
EM: Round [274] log likelihood: -7264.207030
EM: Round [275] log likelihood: -7264.202992
EM: Round [276] log likelihood: -7264.198974
EM: Round [277] log likelihood: -7264.194976
EM: Round [278] log likelihood: -7264.190998
EM: Round [279] log likelihood: -7264.187039
EM: Round [280] log likelihood: -7264.183101
EM: Round [281] log likelihood: -7264.179181
EM: Round [282] log likelihood: -7264.175281
EM: Round [283] log likelihood: -7264.171399
EM: Round [284] log likelihood: -7264.167537
EM: Round [285] log likelihood: -7264.163694
EM: Round [286] log likelihood: -7264.159869
EM: Round [287] log likelihood: -7264.156063
EM: Round [288] log likelihood: -7264.152276
EM: Round [289] log likelihood: -7264.148507
EM: Round [290] log likelihood: -7264.144756
EM: Round [291] log likelihood: -7264.141023
EM: Round [292] log likelihood: -7264.137308
EM: Round [293] log likelihood: -7264.133611
EM: Round [294] log likelihood: -7264.129931
EM: Round [295] log likelihood: -7264.126270
EM: Round [296] log likelihood: -7264.122626
EM: Round [297] log likelihood: -7264.118999
EM: Round [298] log likelihood: -7264.115389
EM: Round [299] log likelihood: -7264.111797
EM: Round [300] log likelihood: -7264.108222
EM: Round [301] log likelihood: -7264.104663
EM: Round [302] log likelihood: -7264.101122
EM: Round [303] log likelihood: -7264.097597
EM: Round [304] log likelihood: -7264.094089
EM: Round [305] log likelihood: -7264.090597
EM: Round [306] log likelihood: -7264.087122
EM: Round [307] log likelihood: -7264.083663
EM: Round [308] log likelihood: -7264.080220
EM: Round [309] log likelihood: -7264.076793
EM: Round [310] log likelihood: -7264.073382
EM: Round [311] log likelihood: -7264.069988
EM: Round [312] log likelihood: -7264.066608
EM: Round [313] log likelihood: -7264.063245
EM: Round [314] log likelihood: -7264.059897
EM: Round [315] log likelihood: -7264.056565
EM: Round [316] log likelihood: -7264.053248
EM: Round [317] log likelihood: -7264.049946
EM: Round [318] log likelihood: -7264.046660
EM: Round [319] log likelihood: -7264.043388
EM: Round [320] log likelihood: -7264.040132
EM: Round [321] log likelihood: -7264.036890
EM: Round [322] log likelihood: -7264.033663
EM: Round [323] log likelihood: -7264.030451
EM: Round [324] log likelihood: -7264.027254
EM: Round [325] log likelihood: -7264.024071
EM: Round [326] log likelihood: -7264.020903
EM: Round [327] log likelihood: -7264.017749
EM: Round [328] log likelihood: -7264.014609
EM: Round [329] log likelihood: -7264.011484
EM: Round [330] log likelihood: -7264.008372
EM: Round [331] log likelihood: -7264.005275
EM: Round [332] log likelihood: -7264.002191
EM: Round [333] log likelihood: -7263.999122
EM: Round [334] log likelihood: -7263.996066
EM: Round [335] log likelihood: -7263.993024
EM: Round [336] log likelihood: -7263.989995
EM: Round [337] log likelihood: -7263.986980
EM: Round [338] log likelihood: -7263.983979
EM: Round [339] log likelihood: -7263.980990
EM: Round [340] log likelihood: -7263.978015
EM: Round [341] log likelihood: -7263.975054
EM: Round [342] log likelihood: -7263.972105
EM: Round [343] log likelihood: -7263.969169
EM: Round [344] log likelihood: -7263.966247
EM: Round [345] log likelihood: -7263.963337
EM: Round [346] log likelihood: -7263.960440
EM: Round [347] log likelihood: -7263.957556
EM: Round [348] log likelihood: -7263.954684
EM: Round [349] log likelihood: -7263.951826
EM: Round [350] log likelihood: -7263.948979
EM: Round [351] log likelihood: -7263.946145
EM: Round [352] log likelihood: -7263.943324
EM: Round [353] log likelihood: -7263.940514
EM: Round [354] log likelihood: -7263.937717
EM: Round [355] log likelihood: -7263.934933
EM: Round [356] log likelihood: -7263.932160
EM: Round [357] log likelihood: -7263.929399
EM: Round [358] log likelihood: -7263.926650
EM: Round [359] log likelihood: -7263.923913
EM: Round [360] log likelihood: -7263.921188
EM: Round [361] log likelihood: -7263.918475
EM: Round [362] log likelihood: -7263.915773
EM: Round [363] log likelihood: -7263.913083
EM: Round [364] log likelihood: -7263.910405
EM: Round [365] log likelihood: -7263.907738
EM: Round [366] log likelihood: -7263.905082
EM: Round [367] log likelihood: -7263.902438
EM: Round [368] log likelihood: -7263.899805
EM: Round [369] log likelihood: -7263.897184
EM: Round [370] log likelihood: -7263.894573
EM: Round [371] log likelihood: -7263.891974
EM: Round [372] log likelihood: -7263.889386
EM: Round [373] log likelihood: -7263.886808
EM: Round [374] log likelihood: -7263.884242
EM: Round [375] log likelihood: -7263.881686
EM: Round [376] log likelihood: -7263.879142
EM: Round [377] log likelihood: -7263.876608
EM: Round [378] log likelihood: -7263.874085
EM: Round [379] log likelihood: -7263.871572
EM: Round [380] log likelihood: -7263.869070
EM: Round [381] log likelihood: -7263.866578
EM: Round [382] log likelihood: -7263.864097
EM: Round [383] log likelihood: -7263.861626
EM: Round [384] log likelihood: -7263.859166
EM: Round [385] log likelihood: -7263.856716
EM: Round [386] log likelihood: -7263.854276
EM: Round [387] log likelihood: -7263.851847
EM: Round [388] log likelihood: -7263.849427
EM: Round [389] log likelihood: -7263.847018
EM: Round [390] log likelihood: -7263.844618
EM: Round [391] log likelihood: -7263.842229
EM: Round [392] log likelihood: -7263.839849
EM: Round [393] log likelihood: -7263.837479
EM: Round [394] log likelihood: -7263.835119
EM: Round [395] log likelihood: -7263.832769
EM: Round [396] log likelihood: -7263.830429
EM: Round [397] log likelihood: -7263.828098
EM: Round [398] log likelihood: -7263.825777
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EM: Round [856] log likelihood: -7263.316059
EM: Round [857] log likelihood: -7263.315598
EM: Round [858] log likelihood: -7263.315138
EM: Round [859] log likelihood: -7263.314679
EM: Round [860] log likelihood: -7263.314222
EM: Round [861] log likelihood: -7263.313767
EM: Round [862] log likelihood: -7263.313313
EM: Round [863] log likelihood: -7263.312860
EM: Round [864] log likelihood: -7263.312409
EM: Round [865] log likelihood: -7263.311959
EM: Round [866] log likelihood: -7263.311510
EM: Round [867] log likelihood: -7263.311063
EM: Round [868] log likelihood: -7263.310618
EM: Round [869] log likelihood: -7263.310174
EM: Round [870] log likelihood: -7263.309731
EM: Round [871] log likelihood: -7263.309290
EM: Round [872] log likelihood: -7263.308850
EM: Round [873] log likelihood: -7263.308411
EM: Round [874] log likelihood: -7263.307974
EM: Round [875] log likelihood: -7263.307539
EM: Round [876] log likelihood: -7263.307104
EM: Round [877] log likelihood: -7263.306671
EM: Round [878] log likelihood: -7263.306240
EM: Round [879] log likelihood: -7263.305810
EM: Round [880] log likelihood: -7263.305381
EM: Round [881] log likelihood: -7263.304953
EM: Round [882] log likelihood: -7263.304527
EM: Round [883] log likelihood: -7263.304102
EM: Round [884] log likelihood: -7263.303679
EM: Round [885] log likelihood: -7263.303257
EM: Round [886] log likelihood: -7263.302836
EM: Round [887] log likelihood: -7263.302417
EM: Round [888] log likelihood: -7263.301999
EM: Round [889] log likelihood: -7263.301582
EM: Round [890] log likelihood: -7263.301166
EM: Round [891] log likelihood: -7263.300752
EM: Round [892] log likelihood: -7263.300339
EM: Round [893] log likelihood: -7263.299928
EM: Round [894] log likelihood: -7263.299518
EM: Round [895] log likelihood: -7263.299109
EM: Round [896] log likelihood: -7263.298701
EM: Round [897] log likelihood: -7263.298295
EM: Round [898] log likelihood: -7263.297890
EM: Round [899] log likelihood: -7263.297486
EM: Round [900] log likelihood: -7263.297083
EM: Round [901] log likelihood: -7263.296682
EM: Round [902] log likelihood: -7263.296282
EM: Round [903] log likelihood: -7263.295884
EM: Round [904] log likelihood: -7263.295486
EM: Round [905] log likelihood: -7263.295090
EM: Round [906] log likelihood: -7263.294695
EM: Round [907] log likelihood: -7263.294301
EM: Round [908] log likelihood: -7263.293909
EM: Round [909] log likelihood: -7263.293518
EM: Round [910] log likelihood: -7263.293128
EM: Round [911] log likelihood: -7263.292739
EM: Round [912] log likelihood: -7263.292351
EM: Round [913] log likelihood: -7263.291965
EM: Round [914] log likelihood: -7263.291580
EM: Round [915] log likelihood: -7263.291196
EM: Round [916] log likelihood: -7263.290814
EM: Round [917] log likelihood: -7263.290432
EM: Round [918] log likelihood: -7263.290052
EM: Round [919] log likelihood: -7263.289673
EM: Round [920] log likelihood: -7263.289295
EM: Round [921] log likelihood: -7263.288918
EM: Round [922] log likelihood: -7263.288543
EM: Round [923] log likelihood: -7263.288168
EM: Round [924] log likelihood: -7263.287795
EM: Round [925] log likelihood: -7263.287423
EM: Round [926] log likelihood: -7263.287053
EM: Round [927] log likelihood: -7263.286683
EM: Round [928] log likelihood: -7263.286315
EM: Round [929] log likelihood: -7263.285947
EM: Round [930] log likelihood: -7263.285581
EM: Round [931] log likelihood: -7263.285216
EM: Round [932] log likelihood: -7263.284852
EM: Round [933] log likelihood: -7263.284489
EM: Round [934] log likelihood: -7263.284128
EM: Round [935] log likelihood: -7263.283767
EM: Round [936] log likelihood: -7263.283408
EM: Round [937] log likelihood: -7263.283050
EM: Round [938] log likelihood: -7263.282693
EM: Round [939] log likelihood: -7263.282337
EM: Round [940] log likelihood: -7263.281982
EM: Round [941] log likelihood: -7263.281628
EM: Round [942] log likelihood: -7263.281276
EM: Round [943] log likelihood: -7263.280924
EM: Round [944] log likelihood: -7263.280574
EM: Round [945] log likelihood: -7263.280225
EM: Round [946] log likelihood: -7263.279876
EM: Round [947] log likelihood: -7263.279529
EM: Round [948] log likelihood: -7263.279183
EM: Round [949] log likelihood: -7263.278838
EM: Round [950] log likelihood: -7263.278495
EM: Round [951] log likelihood: -7263.278152
EM: Round [952] log likelihood: -7263.277810
EM: Round [953] log likelihood: -7263.277469
EM: Round [954] log likelihood: -7263.277130
EM: Round [955] log likelihood: -7263.276791
EM: Round [956] log likelihood: -7263.276454
EM: Round [957] log likelihood: -7263.276117
EM: Round [958] log likelihood: -7263.275782
EM: Round [959] log likelihood: -7263.275448
EM: Round [960] log likelihood: -7263.275115
EM: Round [961] log likelihood: -7263.274782
EM: Round [962] log likelihood: -7263.274451
EM: Round [963] log likelihood: -7263.274121
EM: Round [964] log likelihood: -7263.273792
EM: Round [965] log likelihood: -7263.273464
EM: Round [966] log likelihood: -7263.273137
EM: Round [967] log likelihood: -7263.272811
EM: Round [968] log likelihood: -7263.272486
EM: Round [969] log likelihood: -7263.272162
EM: Round [970] log likelihood: -7263.271839
EM: Round [971] log likelihood: -7263.271517
EM: Round [972] log likelihood: -7263.271196
EM: Round [973] log likelihood: -7263.270876
EM: Round [974] log likelihood: -7263.270557
EM: Round [975] log likelihood: -7263.270239
EM: Round [976] log likelihood: -7263.269922
EM: Round [977] log likelihood: -7263.269606
EM: Round [978] log likelihood: -7263.269291
EM: Round [979] log likelihood: -7263.268977
EM: Round [980] log likelihood: -7263.268664
EM: Round [981] log likelihood: -7263.268351
EM: Round [982] log likelihood: -7263.268040
EM: Round [983] log likelihood: -7263.267730
EM: Round [984] log likelihood: -7263.267421
EM: Round [985] log likelihood: -7263.267113
EM: Round [986] log likelihood: -7263.266806
EM: Round [987] log likelihood: -7263.266499
EM: Round [988] log likelihood: -7263.266194
EM: Round [989] log likelihood: -7263.265889
EM: Round [990] log likelihood: -7263.265586
EM: Round [991] log likelihood: -7263.265283
EM: Round [992] log likelihood: -7263.264982
EM: Round [993] log likelihood: -7263.264681
EM: Round [994] log likelihood: -7263.264382
EM: Round [995] log likelihood: -7263.264083
EM: Round [996] log likelihood: -7263.263785
EM: Round [997] log likelihood: -7263.263488
EM: Round [998] log likelihood: -7263.263192
EM: Round [999] log likelihood: -7263.262897
EM: Round [1000] log likelihood: -7263.262603
EM: Round [1001] log likelihood: -7263.262309
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/fi_workdir/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir
-done, see /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5665.502275
EM: Round [1] log likelihood: -5665.471152
EM: Round [2] log likelihood: -5665.471008
EM: Round [3] log likelihood: -5665.471004
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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 294468238
Execution Time = 5.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gtf  > /tmp/nxf.4edL9IDkmh/fi_workdir/microH.dat
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.4edL9IDkmh/fi_workdir/microH.dat /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/fi_workdir/microH.dat /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.4edL9IDkmh --json_outfile /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_Q7O_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.4edL9IDkmh --json_outfile /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1
Running: touch /tmp/nxf.4edL9IDkmh/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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir > /tmp/nxf.4edL9IDkmh/1173_Q7O_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.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000230092.7]
WARNING, no entry stored in dbm for [ENSG00000185596.16]
WARNING, no entry stored in dbm for [ENSG00000233806.7]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.4edL9IDkmh/ctat_genome_lib_build_dir > /tmp/nxf.4edL9IDkmh/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.4edL9IDkmh/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory