Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/4f2779c074c6d7b12b49b208933ecf/tih_rna_sample_00764_B23MVV7LT4_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/a0/5b407c68f14806be4125fafa62b823/tih_rna_sample_00764_B23MVV7LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/63246d4028df7aab7b6236d7980bbc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/5b407c68f14806be4125fafa62b823/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/63246d4028df7aab7b6236d7980bbc/.command.run
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00764_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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 tih_rna_sample_00764_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf > /tmp/nxf.Kj68ZgUQ3V/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf > /tmp/nxf.Kj68ZgUQ3V/cytoBand.txt
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00764_B23MVV7LT4_1.star --out_dir /tmp/nxf.Kj68ZgUQ3V/fi_workdir --reads "/tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:02:10 ..... started STAR run
Jun 08 10:02:10 ..... loading genome
Jun 08 10:03:52 ... generating Suffix Array index
Jun 08 10:07:35 ... completed Suffix Array index
Jun 08 10:07:35 ..... processing annotations GTF
Jun 08 10:07:35 ..... inserting junctions into the genome indices
Jun 08 10:08:36 ..... started mapping
Jun 08 10:53:48 ..... finished mapping
Jun 08 10:53:50 ..... started sorting BAM
Jun 08 10:53:51 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00764_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00764_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 51.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00764_B23MVV7LT4_1.star --out_dir /tmp/nxf.Kj68ZgUQ3V/fi_workdir --reads "/tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
10:54:15 : INFO : Done.
Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[4030000]   -done parsing /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          ' ** passed ** ' => 26951,
          'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 12,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 372,
          'excessive soft clipping' => 25444,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 84,
          'per_id < 96' => 11477,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 16,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 407,
          'seq-similar region overlap' => 610,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num genes matched < 2' => 119,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 44,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 29,
          'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 38,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 340,
          'small anchor length' => 103,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 75,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 3,
          'low complexity anchor region' => 20
        };
-writing fusion junction support info.
Execution Time = 2.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[6000]   -fusion SPANNING read extraction for scaff: AC000067.1--TXNRD2

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[8000]   -fusion SPANNING read extraction for scaff: AC245452.1--TXNRD2

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[1025000]   
[1026000]   
[1027000]   -fusion SPANNING read extraction for scaff: AL591378.1--DMD

[1000]   
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[250000]   
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[253000]   
[254000]   
[255000]   
[256000]   -fusion SPANNING read extraction for scaff: BMPR1A--ACTA2

[1000]   -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   -fusion SPANNING read extraction for scaff: FNDC3A--AC098862.1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   -fusion SPANNING read extraction for scaff: FNDC3A--SLIT2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[20000]   
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[100000]   
[101000]   
[102000]   
[103000]   
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[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   -fusion SPANNING read extraction for scaff: MAPK1--TXNRD2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[14000]   
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[20000]   
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[37000]   
[38000]   
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[40000]   
[41000]   
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[44000]   
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[50000]   
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[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[20000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[18000]   
[19000]   
[20000]   
[21000]   
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[23000]   
[24000]   
[25000]   
[26000]   
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[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
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[24000]   
[25000]   
[26000]   
[27000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[20000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[20000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: PCDHA2--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[20000]   
[21000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[20000]   
[21000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[20000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[30000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[30000]   
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[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
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[20000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[36000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA10

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[32000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB6

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[45000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA11

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[33000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB7

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[40000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA12

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[38000]   
[39000]   -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA9

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[22000]   -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146

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[194000]   -fusion SPANNING read extraction for scaff: PPIL2--AC007326.5

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[188000]   
[189000]   -fusion SPANNING read extraction for scaff: PPIL2--AL353807.5

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[186000]   
[187000]   -fusion SPANNING read extraction for scaff: PPIL2--ERVK-28

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[187000]   -fusion SPANNING read extraction for scaff: PPIL2--AC087354.1

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[185000]   -fusion SPANNING read extraction for scaff: PPIL2--LHFPL3-AS1

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[188000]   -fusion SPANNING read extraction for scaff: PPIL2--AC084198.1

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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PTEN--ATAD1

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[60000]   
[61000]   -fusion SPANNING read extraction for scaff: RB1--FNDC3A

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[20000]   -fusion SPANNING read extraction for scaff: RB1--GPC5

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[20000]   -fusion SPANNING read extraction for scaff: RB1--LINC00363

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[34000]   
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[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: SEPTIN5--TXNRD2

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[50000]   
[51000]   -fusion SPANNING read extraction for scaff: SLIT2--PSME2P2

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[48000]   
[49000]   -fusion SPANNING read extraction for scaff: SLIT2--AL161421.1

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[25000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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

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[60000]   -fusion SPANNING read extraction for scaff: TMCO3--TP53

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[59000]   -fusion SPANNING read extraction for scaff: TP53--TMCO3

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[5000]   -fusion SPANNING read extraction for scaff: TTC9C--SHANK2

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[53000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[12000]   -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 13335,
          'seq similar region alignment' => 148580
        };
Execution Time = 6.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -14485.101537
EM: Round [1] log likelihood: -14110.147082
EM: Round [2] log likelihood: -13951.152027
EM: Round [3] log likelihood: -13872.878025
EM: Round [4] log likelihood: -13830.828361
EM: Round [5] log likelihood: -13806.453411
EM: Round [6] log likelihood: -13791.393481
EM: Round [7] log likelihood: -13781.552986
EM: Round [8] log likelihood: -13774.810392
EM: Round [9] log likelihood: -13770.029702
EM: Round [10] log likelihood: -13766.567568
EM: Round [11] log likelihood: -13764.027877
EM: Round [12] log likelihood: -13762.147880
EM: Round [13] log likelihood: -13760.745130
EM: Round [14] log likelihood: -13759.689951
EM: Round [15] log likelihood: -13758.889111
EM: Round [16] log likelihood: -13758.275161
EM: Round [17] log likelihood: -13757.799116
EM: Round [18] log likelihood: -13757.425295
EM: Round [19] log likelihood: -13757.127637
EM: Round [20] log likelihood: -13756.887062
EM: Round [21] log likelihood: -13756.689557
EM: Round [22] log likelihood: -13756.524805
EM: Round [23] log likelihood: -13756.385179
EM: Round [24] log likelihood: -13756.265021
EM: Round [25] log likelihood: -13756.160118
EM: Round [26] log likelihood: -13756.067312
EM: Round [27] log likelihood: -13755.984228
EM: Round [28] log likelihood: -13755.909063
EM: Round [29] log likelihood: -13755.840442
EM: Round [30] log likelihood: -13755.777307
EM: Round [31] log likelihood: -13755.718837
EM: Round [32] log likelihood: -13755.664386
EM: Round [33] log likelihood: -13755.613444
EM: Round [34] log likelihood: -13755.565602
EM: Round [35] log likelihood: -13755.520527
EM: Round [36] log likelihood: -13755.477946
EM: Round [37] log likelihood: -13755.437633
EM: Round [38] log likelihood: -13755.399397
EM: Round [39] log likelihood: -13755.363075
EM: Round [40] log likelihood: -13755.328527
EM: Round [41] log likelihood: -13755.295630
EM: Round [42] log likelihood: -13755.264277
EM: Round [43] log likelihood: -13755.234372
EM: Round [44] log likelihood: -13755.205829
EM: Round [45] log likelihood: -13755.178572
EM: Round [46] log likelihood: -13755.152528
EM: Round [47] log likelihood: -13755.127633
EM: Round [48] log likelihood: -13755.103828
EM: Round [49] log likelihood: -13755.081058
EM: Round [50] log likelihood: -13755.059271
EM: Round [51] log likelihood: -13755.038420
EM: Round [52] log likelihood: -13755.018461
EM: Round [53] log likelihood: -13754.999350
EM: Round [54] log likelihood: -13754.981050
EM: Round [55] log likelihood: -13754.963522
EM: Round [56] log likelihood: -13754.946732
EM: Round [57] log likelihood: -13754.930647
EM: Round [58] log likelihood: -13754.915235
EM: Round [59] log likelihood: -13754.900467
EM: Round [60] log likelihood: -13754.886314
EM: Round [61] log likelihood: -13754.872749
EM: Round [62] log likelihood: -13754.859748
EM: Round [63] log likelihood: -13754.847285
EM: Round [64] log likelihood: -13754.835338
EM: Round [65] log likelihood: -13754.823884
EM: Round [66] log likelihood: -13754.812902
EM: Round [67] log likelihood: -13754.802373
EM: Round [68] log likelihood: -13754.792277
EM: Round [69] log likelihood: -13754.782596
EM: Round [70] log likelihood: -13754.773313
EM: Round [71] log likelihood: -13754.764410
EM: Round [72] log likelihood: -13754.755872
EM: Round [73] log likelihood: -13754.747684
EM: Round [74] log likelihood: -13754.739830
EM: Round [75] log likelihood: -13754.732298
EM: Round [76] log likelihood: -13754.725073
EM: Round [77] log likelihood: -13754.718144
EM: Round [78] log likelihood: -13754.711497
EM: Round [79] log likelihood: -13754.705121
EM: Round [80] log likelihood: -13754.699004
EM: Round [81] log likelihood: -13754.693137
EM: Round [82] log likelihood: -13754.687508
EM: Round [83] log likelihood: -13754.682109
EM: Round [84] log likelihood: -13754.676929
EM: Round [85] log likelihood: -13754.671959
EM: Round [86] log likelihood: -13754.667192
EM: Round [87] log likelihood: -13754.662617
EM: Round [88] log likelihood: -13754.658229
EM: Round [89] log likelihood: -13754.654019
EM: Round [90] log likelihood: -13754.649979
EM: Round [91] log likelihood: -13754.646103
EM: Round [92] log likelihood: -13754.642384
EM: Round [93] log likelihood: -13754.638816
EM: Round [94] log likelihood: -13754.635392
EM: Round [95] log likelihood: -13754.632107
EM: Round [96] log likelihood: -13754.628954
EM: Round [97] log likelihood: -13754.625930
EM: Round [98] log likelihood: -13754.623027
EM: Round [99] log likelihood: -13754.620242
EM: Round [100] log likelihood: -13754.617570
EM: Round [101] log likelihood: -13754.615005
EM: Round [102] log likelihood: -13754.612545
EM: Round [103] log likelihood: -13754.610183
EM: Round [104] log likelihood: -13754.607917
EM: Round [105] log likelihood: -13754.605742
EM: Round [106] log likelihood: -13754.603656
EM: Round [107] log likelihood: -13754.601653
EM: Round [108] log likelihood: -13754.599731
EM: Round [109] log likelihood: -13754.597887
EM: Round [110] log likelihood: -13754.596117
EM: Round [111] log likelihood: -13754.594419
EM: Round [112] log likelihood: -13754.592788
EM: Round [113] log likelihood: -13754.591224
EM: Round [114] log likelihood: -13754.589723
EM: Round [115] log likelihood: -13754.588282
EM: Round [116] log likelihood: -13754.586899
EM: Round [117] log likelihood: -13754.585572
EM: Round [118] log likelihood: -13754.584298
EM: Round [119] log likelihood: -13754.583076
EM: Round [120] log likelihood: -13754.581903
EM: Round [121] log likelihood: -13754.580777
EM: Round [122] log likelihood: -13754.579696
EM: Round [123] log likelihood: -13754.578659
EM: Round [124] log likelihood: -13754.577664
EM: Round [125] log likelihood: -13754.576708
EM: Round [126] log likelihood: -13754.575791
EM: Round [127] log likelihood: -13754.574911
EM: Round [128] log likelihood: -13754.574066
EM: Round [129] log likelihood: -13754.573255
EM: Round [130] log likelihood: -13754.572477
EM: Round [131] log likelihood: -13754.571730
EM: Round [132] log likelihood: -13754.571013
EM: Round [133] log likelihood: -13754.570325
EM: Round [134] log likelihood: -13754.569664
EM: Round [135] log likelihood: -13754.569030
EM: Round [136] log likelihood: -13754.568422
EM: Round [137] log likelihood: -13754.567838
EM: Round [138] log likelihood: -13754.567277
EM: Round [139] log likelihood: -13754.566739
EM: Round [140] log likelihood: -13754.566222
EM: Round [141] log likelihood: -13754.565726
EM: Round [142] log likelihood: -13754.565250
EM: Round [143] log likelihood: -13754.564793
EM: Round [144] log likelihood: -13754.564355
EM: Round [145] log likelihood: -13754.563934
EM: Round [146] log likelihood: -13754.563529
EM: Round [147] log likelihood: -13754.563141
EM: Round [148] log likelihood: -13754.562769
EM: Round [149] log likelihood: -13754.562411
EM: Round [150] log likelihood: -13754.562068
EM: Round [151] log likelihood: -13754.561738
EM: Round [152] log likelihood: -13754.561422
EM: Round [153] log likelihood: -13754.561118
EM: Round [154] log likelihood: -13754.560827
EM: Round [155] log likelihood: -13754.560547
EM: Round [156] log likelihood: -13754.560278
EM: Round [157] log likelihood: -13754.560020
EM: Round [158] log likelihood: -13754.559772
EM: Round [159] log likelihood: -13754.559535
EM: Round [160] log likelihood: -13754.559306
EM: Round [161] log likelihood: -13754.559087
EM: Round [162] log likelihood: -13754.558877
EM: Round [163] log likelihood: -13754.558675
EM: Round [164] log likelihood: -13754.558480
EM: Round [165] log likelihood: -13754.558294
EM: Round [166] log likelihood: -13754.558115
EM: Round [167] log likelihood: -13754.557944
EM: Round [168] log likelihood: -13754.557779
EM: Round [169] log likelihood: -13754.557620
EM: Round [170] log likelihood: -13754.557468
EM: Round [171] log likelihood: -13754.557322
EM: Round [172] log likelihood: -13754.557182
EM: Round [173] log likelihood: -13754.557047
EM: Round [174] log likelihood: -13754.556918
EM: Round [175] log likelihood: -13754.556794
EM: Round [176] log likelihood: -13754.556674
EM: Round [177] log likelihood: -13754.556560
EM: Round [178] log likelihood: -13754.556450
EM: Round [179] log likelihood: -13754.556344
EM: Round [180] log likelihood: -13754.556242
EM: Round [181] log likelihood: -13754.556145
EM: Stopping iterations at round 181 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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/tih_rna_sample_00764_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir
-done, see /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -10626.427294
EM: Round [1] log likelihood: -10312.127402
EM: Round [2] log likelihood: -10198.158187
EM: Round [3] log likelihood: -10151.444663
EM: Round [4] log likelihood: -10131.785965
EM: Round [5] log likelihood: -10123.431502
EM: Round [6] log likelihood: -10119.951869
EM: Round [7] log likelihood: -10118.580416
EM: Round [8] log likelihood: -10118.074945
EM: Round [9] log likelihood: -10117.899255
EM: Round [10] log likelihood: -10117.840754
EM: Round [11] log likelihood: -10117.821815
EM: Round [12] log likelihood: -10117.815789
EM: Round [13] log likelihood: -10117.813891
EM: Round [14] log likelihood: -10117.813297
EM: Round [15] log likelihood: -10117.813112
EM: Round [16] log likelihood: -10117.813054
EM: Stopping iterations at round 16 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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz: 245131577
Execution Time = 4.58 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa --gtf /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf  > /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fa --gtf /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf  > /tmp/nxf.Kj68ZgUQ3V/fi_workdir/microH.dat
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.Kj68ZgUQ3V/fi_workdir/microH.dat /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_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.Kj68ZgUQ3V/fi_workdir/microH.dat /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Kj68ZgUQ3V --json_outfile /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00764_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.Kj68ZgUQ3V --json_outfile /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00764_B23MVV7LT4_1
Running: touch /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00764_B23MVV7LT4_1 --html_output /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00764_B23MVV7LT4_1 --html_output /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000284294.1]
WARNING, no entry stored in dbm for [ENSG00000284294.1]
WARNING, no entry stored in dbm for [ENSG00000284294.1]
WARNING, no entry stored in dbm for [ENSG00000267696.6]
WARNING, no entry stored in dbm for [ENSG00000286699.1]
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 [ENSG00000189136.9]
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 [ENSG00000226869.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000232849.2]
WARNING, no entry stored in dbm for [ENSG00000232849.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.Kj68ZgUQ3V/ctat_genome_lib_build_dir > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.Kj68ZgUQ3V/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory