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/33/578219d9780ca6c8a8552426dccbf7/tih_rna_sample_00163_B23WHTKLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/fe09ca710bbbb1cff91bf74619cec3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/578219d9780ca6c8a8552426dccbf7/tih_rna_sample_00163_B23WHTKLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/fe09ca710bbbb1cff91bf74619cec3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/a69e9513655a3813a65626ff2aa7df/tih_rna_sample_00163_B23WHTKLT4_2.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00163_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2 --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 tih_rna_sample_00163_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf > /tmp/nxf.o4DreIYIT5/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf > /tmp/nxf.o4DreIYIT5/cytoBand.txt
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed
-parsing GTF file: /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00163_B23WHTKLT4_2.star --out_dir /tmp/nxf.o4DreIYIT5/fi_workdir --reads "/tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:08:38 ..... started STAR run
Jun 08 10:08:38 ..... loading genome
Jun 08 10:10:30 ... generating Suffix Array index
Jun 08 10:14:27 ... completed Suffix Array index
Jun 08 10:14:27 ..... processing annotations GTF
Jun 08 10:14:27 ..... inserting junctions into the genome indices
Jun 08 10:15:28 ..... started mapping
Jun 08 11:30:59 ..... finished mapping
Jun 08 11:31:01 ..... started sorting BAM
Jun 08 11:31:02 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00163_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00163_B23WHTKLT4_2.star.sortedByCoord.out.bam
Execution Time = 82.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00163_B23WHTKLT4_2.star --out_dir /tmp/nxf.o4DreIYIT5/fi_workdir --reads "/tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
11:31:11 : INFO : Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[1310000]   -done parsing /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 10276,
          'low complexity anchor region' => 21,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 120,
          ' ** passed ** ' => 5058,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 42,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 46,
          'num genes matched < 2' => 53,
          'small anchor length' => 1,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
          'per_id < 96' => 6234,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 102,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 9,
          'seq-similar region overlap' => 364
        };
-writing fusion junction support info.
Execution Time = 0.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[356000]   
[357000]   -fusion SPANNING read extraction for scaff: PIP4K2B--CDK12

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[54000]   
[55000]   -fusion SPANNING read extraction for scaff: RAB31--CBLB

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: RAB31--AC131237.1

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[134000]   -fusion SPANNING read extraction for scaff: RUNX1--LINC01674

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[166000]   -fusion SPANNING read extraction for scaff: RUNX1--POTED

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[133000]   -fusion SPANNING read extraction for scaff: RUNX1--GTF2IP2

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[109000]   -fusion SPANNING read extraction for scaff: SCARF2--EHMT1

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[97000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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

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[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[37000]   
[38000]   -fusion SPANNING read extraction for scaff: TPD52L1--HDDC2

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[20000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[23000]   -fusion SPANNING read extraction for scaff: ZNF44--AC024563.1
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 15640,
          'lacks exon overlap' => 11170
        };
Execution Time = 1.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -7172.498939
EM: Round [1] log likelihood: -7167.511972
EM: Round [2] log likelihood: -7167.204556
EM: Round [3] log likelihood: -7166.934925
EM: Round [4] log likelihood: -7166.694895
EM: Round [5] log likelihood: -7166.480515
EM: Round [6] log likelihood: -7166.288491
EM: Round [7] log likelihood: -7166.116051
EM: Round [8] log likelihood: -7165.960843
EM: Round [9] log likelihood: -7165.820854
EM: Round [10] log likelihood: -7165.694356
EM: Round [11] log likelihood: -7165.579849
EM: Round [12] log likelihood: -7165.476032
EM: Round [13] log likelihood: -7165.381767
EM: Round [14] log likelihood: -7165.296055
EM: Round [15] log likelihood: -7165.218018
EM: Round [16] log likelihood: -7165.146879
EM: Round [17] log likelihood: -7165.081949
EM: Round [18] log likelihood: -7165.022619
EM: Round [19] log likelihood: -7164.968342
EM: Round [20] log likelihood: -7164.918633
EM: Round [21] log likelihood: -7164.873056
EM: Round [22] log likelihood: -7164.831223
EM: Round [23] log likelihood: -7164.792783
EM: Round [24] log likelihood: -7164.757421
EM: Round [25] log likelihood: -7164.724855
EM: Round [26] log likelihood: -7164.694829
EM: Round [27] log likelihood: -7164.667113
EM: Round [28] log likelihood: -7164.641498
EM: Round [29] log likelihood: -7164.617798
EM: Round [30] log likelihood: -7164.595840
EM: Round [31] log likelihood: -7164.575471
EM: Round [32] log likelihood: -7164.556552
EM: Round [33] log likelihood: -7164.538955
EM: Round [34] log likelihood: -7164.522565
EM: Round [35] log likelihood: -7164.507278
EM: Round [36] log likelihood: -7164.492999
EM: Round [37] log likelihood: -7164.479641
EM: Round [38] log likelihood: -7164.467126
EM: Round [39] log likelihood: -7164.455383
EM: Round [40] log likelihood: -7164.444345
EM: Round [41] log likelihood: -7164.433955
EM: Round [42] log likelihood: -7164.424159
EM: Round [43] log likelihood: -7164.414906
EM: Round [44] log likelihood: -7164.406153
EM: Round [45] log likelihood: -7164.397858
EM: Round [46] log likelihood: -7164.389985
EM: Round [47] log likelihood: -7164.382498
EM: Round [48] log likelihood: -7164.375369
EM: Round [49] log likelihood: -7164.368567
EM: Round [50] log likelihood: -7164.362067
EM: Round [51] log likelihood: -7164.355847
EM: Round [52] log likelihood: -7164.349883
EM: Round [53] log likelihood: -7164.344157
EM: Round [54] log likelihood: -7164.338650
EM: Round [55] log likelihood: -7164.333347
EM: Round [56] log likelihood: -7164.328231
EM: Round [57] log likelihood: -7164.323290
EM: Round [58] log likelihood: -7164.318511
EM: Round [59] log likelihood: -7164.313882
EM: Round [60] log likelihood: -7164.309393
EM: Round [61] log likelihood: -7164.305034
EM: Round [62] log likelihood: -7164.300796
EM: Round [63] log likelihood: -7164.296672
EM: Round [64] log likelihood: -7164.292654
EM: Round [65] log likelihood: -7164.288735
EM: Round [66] log likelihood: -7164.284908
EM: Round [67] log likelihood: -7164.281169
EM: Round [68] log likelihood: -7164.277512
EM: Round [69] log likelihood: -7164.273932
EM: Round [70] log likelihood: -7164.270425
EM: Round [71] log likelihood: -7164.266987
EM: Round [72] log likelihood: -7164.263614
EM: Round [73] log likelihood: -7164.260302
EM: Round [74] log likelihood: -7164.257048
EM: Round [75] log likelihood: -7164.253850
EM: Round [76] log likelihood: -7164.250705
EM: Round [77] log likelihood: -7164.247611
EM: Round [78] log likelihood: -7164.244564
EM: Round [79] log likelihood: -7164.241563
EM: Round [80] log likelihood: -7164.238606
EM: Round [81] log likelihood: -7164.235692
EM: Round [82] log likelihood: -7164.232818
EM: Round [83] log likelihood: -7164.229983
EM: Round [84] log likelihood: -7164.227186
EM: Round [85] log likelihood: -7164.224425
EM: Round [86] log likelihood: -7164.221698
EM: Round [87] log likelihood: -7164.219006
EM: Round [88] log likelihood: -7164.216347
EM: Round [89] log likelihood: -7164.213719
EM: Round [90] log likelihood: -7164.211122
EM: Round [91] log likelihood: -7164.208555
EM: Round [92] log likelihood: -7164.206017
EM: Round [93] log likelihood: -7164.203508
EM: Round [94] log likelihood: -7164.201026
EM: Round [95] log likelihood: -7164.198571
EM: Round [96] log likelihood: -7164.196143
EM: Round [97] log likelihood: -7164.193740
EM: Round [98] log likelihood: -7164.191362
EM: Round [99] log likelihood: -7164.189010
EM: Round [100] log likelihood: -7164.186681
EM: Round [101] log likelihood: -7164.184376
EM: Round [102] log likelihood: -7164.182094
EM: Round [103] log likelihood: -7164.179835
EM: Round [104] log likelihood: -7164.177598
EM: Round [105] log likelihood: -7164.175383
EM: Round [106] log likelihood: -7164.173190
EM: Round [107] log likelihood: -7164.171018
EM: Round [108] log likelihood: -7164.168867
EM: Round [109] log likelihood: -7164.166736
EM: Round [110] log likelihood: -7164.164625
EM: Round [111] log likelihood: -7164.162535
EM: Round [112] log likelihood: -7164.160464
EM: Round [113] log likelihood: -7164.158412
EM: Round [114] log likelihood: -7164.156380
EM: Round [115] log likelihood: -7164.154366
EM: Round [116] log likelihood: -7164.152371
EM: Round [117] log likelihood: -7164.150394
EM: Round [118] log likelihood: -7164.148435
EM: Round [119] log likelihood: -7164.146494
EM: Round [120] log likelihood: -7164.144571
EM: Round [121] log likelihood: -7164.142665
EM: Round [122] log likelihood: -7164.140776
EM: Round [123] log likelihood: -7164.138904
EM: Round [124] log likelihood: -7164.137048
EM: Round [125] log likelihood: -7164.135209
EM: Round [126] log likelihood: -7164.133387
EM: Round [127] log likelihood: -7164.131581
EM: Round [128] log likelihood: -7164.129790
EM: Round [129] log likelihood: -7164.128016
EM: Round [130] log likelihood: -7164.126257
EM: Round [131] log likelihood: -7164.124513
EM: Round [132] log likelihood: -7164.122785
EM: Round [133] log likelihood: -7164.121071
EM: Round [134] log likelihood: -7164.119373
EM: Round [135] log likelihood: -7164.117689
EM: Round [136] log likelihood: -7164.116020
EM: Round [137] log likelihood: -7164.114365
EM: Round [138] log likelihood: -7164.112725
EM: Round [139] log likelihood: -7164.111099
EM: Round [140] log likelihood: -7164.109486
EM: Round [141] log likelihood: -7164.107888
EM: Round [142] log likelihood: -7164.106303
EM: Round [143] log likelihood: -7164.104732
EM: Round [144] log likelihood: -7164.103174
EM: Round [145] log likelihood: -7164.101629
EM: Round [146] log likelihood: -7164.100098
EM: Round [147] log likelihood: -7164.098579
EM: Round [148] log likelihood: -7164.097074
EM: Round [149] log likelihood: -7164.095581
EM: Round [150] log likelihood: -7164.094100
EM: Round [151] log likelihood: -7164.092632
EM: Round [152] log likelihood: -7164.091177
EM: Round [153] log likelihood: -7164.089733
EM: Round [154] log likelihood: -7164.088302
EM: Round [155] log likelihood: -7164.086883
EM: Round [156] log likelihood: -7164.085476
EM: Round [157] log likelihood: -7164.084080
EM: Round [158] log likelihood: -7164.082696
EM: Round [159] log likelihood: -7164.081323
EM: Round [160] log likelihood: -7164.079962
EM: Round [161] log likelihood: -7164.078613
EM: Round [162] log likelihood: -7164.077274
EM: Round [163] log likelihood: -7164.075946
EM: Round [164] log likelihood: -7164.074630
EM: Round [165] log likelihood: -7164.073324
EM: Round [166] log likelihood: -7164.072029
EM: Round [167] log likelihood: -7164.070745
EM: Round [168] log likelihood: -7164.069471
EM: Round [169] log likelihood: -7164.068208
EM: Round [170] log likelihood: -7164.066955
EM: Round [171] log likelihood: -7164.065712
EM: Round [172] log likelihood: -7164.064480
EM: Round [173] log likelihood: -7164.063257
EM: Round [174] log likelihood: -7164.062045
EM: Round [175] log likelihood: -7164.060842
EM: Round [176] log likelihood: -7164.059649
EM: Round [177] log likelihood: -7164.058466
EM: Round [178] log likelihood: -7164.057293
EM: Round [179] log likelihood: -7164.056128
EM: Round [180] log likelihood: -7164.054974
EM: Round [181] log likelihood: -7164.053829
EM: Round [182] log likelihood: -7164.052693
EM: Round [183] log likelihood: -7164.051566
EM: Round [184] log likelihood: -7164.050448
EM: Round [185] log likelihood: -7164.049339
EM: Round [186] log likelihood: -7164.048239
EM: Round [187] log likelihood: -7164.047148
EM: Round [188] log likelihood: -7164.046066
EM: Round [189] log likelihood: -7164.044992
EM: Round [190] log likelihood: -7164.043927
EM: Round [191] log likelihood: -7164.042871
EM: Round [192] log likelihood: -7164.041823
EM: Round [193] log likelihood: -7164.040783
EM: Round [194] log likelihood: -7164.039752
EM: Round [195] log likelihood: -7164.038729
EM: Round [196] log likelihood: -7164.037714
EM: Round [197] log likelihood: -7164.036707
EM: Round [198] log likelihood: -7164.035708
EM: Round [199] log likelihood: -7164.034717
EM: Round [200] log likelihood: -7164.033734
EM: Round [201] log likelihood: -7164.032758
EM: Round [202] log likelihood: -7164.031790
EM: Round [203] log likelihood: -7164.030830
EM: Round [204] log likelihood: -7164.029878
EM: Round [205] log likelihood: -7164.028933
EM: Round [206] log likelihood: -7164.027995
EM: Round [207] log likelihood: -7164.027065
EM: Round [208] log likelihood: -7164.026143
EM: Round [209] log likelihood: -7164.025227
EM: Round [210] log likelihood: -7164.024319
EM: Round [211] log likelihood: -7164.023417
EM: Round [212] log likelihood: -7164.022523
EM: Round [213] log likelihood: -7164.021636
EM: Round [214] log likelihood: -7164.020756
EM: Round [215] log likelihood: -7164.019882
EM: Round [216] log likelihood: -7164.019016
EM: Round [217] log likelihood: -7164.018156
EM: Round [218] log likelihood: -7164.017303
EM: Round [219] log likelihood: -7164.016456
EM: Round [220] log likelihood: -7164.015617
EM: Round [221] log likelihood: -7164.014783
EM: Round [222] log likelihood: -7164.013956
EM: Round [223] log likelihood: -7164.013136
EM: Round [224] log likelihood: -7164.012322
EM: Round [225] log likelihood: -7164.011514
EM: Round [226] log likelihood: -7164.010713
EM: Round [227] log likelihood: -7164.009917
EM: Round [228] log likelihood: -7164.009128
EM: Round [229] log likelihood: -7164.008345
EM: Round [230] log likelihood: -7164.007568
EM: Round [231] log likelihood: -7164.006797
EM: Round [232] log likelihood: -7164.006032
EM: Round [233] log likelihood: -7164.005273
EM: Round [234] log likelihood: -7164.004519
EM: Round [235] log likelihood: -7164.003772
EM: Round [236] log likelihood: -7164.003030
EM: Round [237] log likelihood: -7164.002294
EM: Round [238] log likelihood: -7164.001563
EM: Round [239] log likelihood: -7164.000839
EM: Round [240] log likelihood: -7164.000119
EM: Round [241] log likelihood: -7163.999405
EM: Round [242] log likelihood: -7163.998697
EM: Round [243] log likelihood: -7163.997994
EM: Round [244] log likelihood: -7163.997297
EM: Round [245] log likelihood: -7163.996604
EM: Round [246] log likelihood: -7163.995917
EM: Round [247] log likelihood: -7163.995236
EM: Round [248] log likelihood: -7163.994559
EM: Round [249] log likelihood: -7163.993888
EM: Round [250] log likelihood: -7163.993221
EM: Round [251] log likelihood: -7163.992560
EM: Round [252] log likelihood: -7163.991904
EM: Round [253] log likelihood: -7163.991253
EM: Round [254] log likelihood: -7163.990607
EM: Round [255] log likelihood: -7163.989965
EM: Round [256] log likelihood: -7163.989329
EM: Round [257] log likelihood: -7163.988697
EM: Round [258] log likelihood: -7163.988070
EM: Round [259] log likelihood: -7163.987448
EM: Round [260] log likelihood: -7163.986831
EM: Round [261] log likelihood: -7163.986218
EM: Round [262] log likelihood: -7163.985610
EM: Round [263] log likelihood: -7163.985006
EM: Round [264] log likelihood: -7163.984407
EM: Round [265] log likelihood: -7163.983813
EM: Round [266] log likelihood: -7163.983223
EM: Round [267] log likelihood: -7163.982637
EM: Round [268] log likelihood: -7163.982056
EM: Round [269] log likelihood: -7163.981479
EM: Round [270] log likelihood: -7163.980907
EM: Round [271] log likelihood: -7163.980338
EM: Round [272] log likelihood: -7163.979774
EM: Round [273] log likelihood: -7163.979215
EM: Round [274] log likelihood: -7163.978659
EM: Round [275] log likelihood: -7163.978108
EM: Round [276] log likelihood: -7163.977561
EM: Round [277] log likelihood: -7163.977018
EM: Round [278] log likelihood: -7163.976479
EM: Round [279] log likelihood: -7163.975944
EM: Round [280] log likelihood: -7163.975413
EM: Round [281] log likelihood: -7163.974886
EM: Round [282] log likelihood: -7163.974363
EM: Round [283] log likelihood: -7163.973843
EM: Round [284] log likelihood: -7163.973328
EM: Round [285] log likelihood: -7163.972817
EM: Round [286] log likelihood: -7163.972309
EM: Round [287] log likelihood: -7163.971805
EM: Round [288] log likelihood: -7163.971305
EM: Round [289] log likelihood: -7163.970808
EM: Round [290] log likelihood: -7163.970316
EM: Round [291] log likelihood: -7163.969827
EM: Round [292] log likelihood: -7163.969341
EM: Round [293] log likelihood: -7163.968859
EM: Round [294] log likelihood: -7163.968381
EM: Round [295] log likelihood: -7163.967906
EM: Round [296] log likelihood: -7163.967435
EM: Round [297] log likelihood: -7163.966968
EM: Round [298] log likelihood: -7163.966503
EM: Round [299] log likelihood: -7163.966043
EM: Round [300] log likelihood: -7163.965585
EM: Round [301] log likelihood: -7163.965131
EM: Round [302] log likelihood: -7163.964681
EM: Round [303] log likelihood: -7163.964233
EM: Round [304] log likelihood: -7163.963789
EM: Round [305] log likelihood: -7163.963348
EM: Round [306] log likelihood: -7163.962911
EM: Round [307] log likelihood: -7163.962477
EM: Round [308] log likelihood: -7163.962046
EM: Round [309] log likelihood: -7163.961618
EM: Round [310] log likelihood: -7163.961193
EM: Round [311] log likelihood: -7163.960772
EM: Round [312] log likelihood: -7163.960353
EM: Round [313] log likelihood: -7163.959938
EM: Round [314] log likelihood: -7163.959525
EM: Round [315] log likelihood: -7163.959116
EM: Round [316] log likelihood: -7163.958710
EM: Round [317] log likelihood: -7163.958306
EM: Round [318] log likelihood: -7163.957906
EM: Round [319] log likelihood: -7163.957509
EM: Round [320] log likelihood: -7163.957114
EM: Round [321] log likelihood: -7163.956722
EM: Round [322] log likelihood: -7163.956334
EM: Round [323] log likelihood: -7163.955948
EM: Round [324] log likelihood: -7163.955565
EM: Round [325] log likelihood: -7163.955184
EM: Round [326] log likelihood: -7163.954807
EM: Round [327] log likelihood: -7163.954432
EM: Round [328] log likelihood: -7163.954060
EM: Round [329] log likelihood: -7163.953691
EM: Round [330] log likelihood: -7163.953324
EM: Round [331] log likelihood: -7163.952961
EM: Round [332] log likelihood: -7163.952599
EM: Round [333] log likelihood: -7163.952241
EM: Round [334] log likelihood: -7163.951885
EM: Round [335] log likelihood: -7163.951531
EM: Round [336] log likelihood: -7163.951181
EM: Round [337] log likelihood: -7163.950832
EM: Round [338] log likelihood: -7163.950487
EM: Round [339] log likelihood: -7163.950144
EM: Round [340] log likelihood: -7163.949803
EM: Round [341] log likelihood: -7163.949465
EM: Round [342] log likelihood: -7163.949129
EM: Round [343] log likelihood: -7163.948796
EM: Round [344] log likelihood: -7163.948465
EM: Round [345] log likelihood: -7163.948136
EM: Round [346] log likelihood: -7163.947810
EM: Round [347] log likelihood: -7163.947487
EM: Round [348] log likelihood: -7163.947165
EM: Round [349] log likelihood: -7163.946846
EM: Round [350] log likelihood: -7163.946529
EM: Round [351] log likelihood: -7163.946215
EM: Round [352] log likelihood: -7163.945903
EM: Round [353] log likelihood: -7163.945593
EM: Round [354] log likelihood: -7163.945285
EM: Round [355] log likelihood: -7163.944980
EM: Round [356] log likelihood: -7163.944677
EM: Round [357] log likelihood: -7163.944376
EM: Round [358] log likelihood: -7163.944077
EM: Round [359] log likelihood: -7163.943781
EM: Round [360] log likelihood: -7163.943486
EM: Round [361] log likelihood: -7163.943194
EM: Round [362] log likelihood: -7163.942903
EM: Round [363] log likelihood: -7163.942615
EM: Round [364] log likelihood: -7163.942329
EM: Round [365] log likelihood: -7163.942045
EM: Round [366] log likelihood: -7163.941763
EM: Round [367] log likelihood: -7163.941483
EM: Round [368] log likelihood: -7163.941206
EM: Round [369] log likelihood: -7163.940930
EM: Round [370] log likelihood: -7163.940656
EM: Round [371] log likelihood: -7163.940384
EM: Round [372] log likelihood: -7163.940114
EM: Round [373] log likelihood: -7163.939846
EM: Round [374] log likelihood: -7163.939580
EM: Round [375] log likelihood: -7163.939316
EM: Round [376] log likelihood: -7163.939054
EM: Round [377] log likelihood: -7163.938793
EM: Round [378] log likelihood: -7163.938535
EM: Round [379] log likelihood: -7163.938278
EM: Round [380] log likelihood: -7163.938023
EM: Round [381] log likelihood: -7163.937770
EM: Round [382] log likelihood: -7163.937519
EM: Round [383] log likelihood: -7163.937270
EM: Round [384] log likelihood: -7163.937022
EM: Round [385] log likelihood: -7163.936777
EM: Round [386] log likelihood: -7163.936533
EM: Round [387] log likelihood: -7163.936291
EM: Round [388] log likelihood: -7163.936050
EM: Round [389] log likelihood: -7163.935811
EM: Round [390] log likelihood: -7163.935574
EM: Round [391] log likelihood: -7163.935339
EM: Round [392] log likelihood: -7163.935105
EM: Round [393] log likelihood: -7163.934873
EM: Round [394] log likelihood: -7163.934643
EM: Round [395] log likelihood: -7163.934414
EM: Round [396] log likelihood: -7163.934187
EM: Round [397] log likelihood: -7163.933962
EM: Round [398] log likelihood: -7163.933738
EM: Round [399] log likelihood: -7163.933516
EM: Round [400] log likelihood: -7163.933295
EM: Round [401] log likelihood: -7163.933076
EM: Round [402] log likelihood: -7163.932859
EM: Round [403] log likelihood: -7163.932643
EM: Round [404] log likelihood: -7163.932429
EM: Round [405] log likelihood: -7163.932216
EM: Round [406] log likelihood: -7163.932005
EM: Round [407] log likelihood: -7163.931795
EM: Round [408] log likelihood: -7163.931587
EM: Round [409] log likelihood: -7163.931380
EM: Round [410] log likelihood: -7163.931175
EM: Round [411] log likelihood: -7163.930971
EM: Round [412] log likelihood: -7163.930768
EM: Round [413] log likelihood: -7163.930568
EM: Round [414] log likelihood: -7163.930368
EM: Round [415] log likelihood: -7163.930170
EM: Round [416] log likelihood: -7163.929973
EM: Round [417] log likelihood: -7163.929778
EM: Round [418] log likelihood: -7163.929584
EM: Round [419] log likelihood: -7163.929392
EM: Round [420] log likelihood: -7163.929201
EM: Round [421] log likelihood: -7163.929011
EM: Round [422] log likelihood: -7163.928823
EM: Round [423] log likelihood: -7163.928636
EM: Round [424] log likelihood: -7163.928450
EM: Round [425] log likelihood: -7163.928265
EM: Round [426] log likelihood: -7163.928082
EM: Round [427] log likelihood: -7163.927901
EM: Round [428] log likelihood: -7163.927720
EM: Round [429] log likelihood: -7163.927541
EM: Round [430] log likelihood: -7163.927363
EM: Round [431] log likelihood: -7163.927186
EM: Round [432] log likelihood: -7163.927011
EM: Round [433] log likelihood: -7163.926837
EM: Round [434] log likelihood: -7163.926664
EM: Round [435] log likelihood: -7163.926492
EM: Round [436] log likelihood: -7163.926322
EM: Round [437] log likelihood: -7163.926153
EM: Round [438] log likelihood: -7163.925985
EM: Round [439] log likelihood: -7163.925818
EM: Round [440] log likelihood: -7163.925652
EM: Round [441] log likelihood: -7163.925488
EM: Round [442] log likelihood: -7163.925324
EM: Round [443] log likelihood: -7163.925162
EM: Round [444] log likelihood: -7163.925001
EM: Round [445] log likelihood: -7163.924842
EM: Round [446] log likelihood: -7163.924683
EM: Round [447] log likelihood: -7163.924525
EM: Round [448] log likelihood: -7163.924369
EM: Round [449] log likelihood: -7163.924213
EM: Round [450] log likelihood: -7163.924059
EM: Round [451] log likelihood: -7163.923906
EM: Round [452] log likelihood: -7163.923754
EM: Round [453] log likelihood: -7163.923603
EM: Round [454] log likelihood: -7163.923453
EM: Round [455] log likelihood: -7163.923304
EM: Round [456] log likelihood: -7163.923156
EM: Round [457] log likelihood: -7163.923010
EM: Round [458] log likelihood: -7163.922864
EM: Round [459] log likelihood: -7163.922719
EM: Round [460] log likelihood: -7163.922576
EM: Round [461] log likelihood: -7163.922433
EM: Round [462] log likelihood: -7163.922291
EM: Round [463] log likelihood: -7163.922151
EM: Round [464] log likelihood: -7163.922011
EM: Round [465] log likelihood: -7163.921873
EM: Round [466] log likelihood: -7163.921735
EM: Round [467] log likelihood: -7163.921598
EM: Round [468] log likelihood: -7163.921463
EM: Round [469] log likelihood: -7163.921328
EM: Round [470] log likelihood: -7163.921194
EM: Round [471] log likelihood: -7163.921061
EM: Round [472] log likelihood: -7163.920929
EM: Round [473] log likelihood: -7163.920798
EM: Round [474] log likelihood: -7163.920668
EM: Round [475] log likelihood: -7163.920539
EM: Round [476] log likelihood: -7163.920411
EM: Round [477] log likelihood: -7163.920284
EM: Round [478] log likelihood: -7163.920157
EM: Round [479] log likelihood: -7163.920032
EM: Round [480] log likelihood: -7163.919907
EM: Round [481] log likelihood: -7163.919783
EM: Round [482] log likelihood: -7163.919660
EM: Round [483] log likelihood: -7163.919538
EM: Round [484] log likelihood: -7163.919417
EM: Round [485] log likelihood: -7163.919297
EM: Round [486] log likelihood: -7163.919178
EM: Round [487] log likelihood: -7163.919059
EM: Round [488] log likelihood: -7163.918941
EM: Round [489] log likelihood: -7163.918824
EM: Round [490] log likelihood: -7163.918708
EM: Round [491] log likelihood: -7163.918593
EM: Round [492] log likelihood: -7163.918478
EM: Round [493] log likelihood: -7163.918365
EM: Round [494] log likelihood: -7163.918252
EM: Round [495] log likelihood: -7163.918140
EM: Round [496] log likelihood: -7163.918029
EM: Round [497] log likelihood: -7163.917918
EM: Round [498] log likelihood: -7163.917808
EM: Round [499] log likelihood: -7163.917699
EM: Round [500] log likelihood: -7163.917591
EM: Round [501] log likelihood: -7163.917484
EM: Round [502] log likelihood: -7163.917377
EM: Round [503] log likelihood: -7163.917271
EM: Round [504] log likelihood: -7163.917166
EM: Round [505] log likelihood: -7163.917062
EM: Round [506] log likelihood: -7163.916958
EM: Round [507] log likelihood: -7163.916855
EM: Round [508] log likelihood: -7163.916753
EM: Round [509] log likelihood: -7163.916652
EM: Round [510] log likelihood: -7163.916551
EM: Round [511] log likelihood: -7163.916451
EM: Round [512] log likelihood: -7163.916351
EM: Stopping iterations at round 512 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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam || : 
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/tih_rna_sample_00163_B23WHTKLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.Pfam.gff3 
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa > /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2 --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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/tih_rna_sample_00163_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir
-done, see /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -6968.903899
EM: Round [1] log likelihood: -6967.186293
EM: Round [2] log likelihood: -6967.185637
EM: Round [3] log likelihood: -6967.185637
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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_1.fastp.fastq.gz: 295174898
Execution Time = 5.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa --gtf /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf  > /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fa --gtf /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.gtf  > /tmp/nxf.o4DreIYIT5/fi_workdir/microH.dat
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.o4DreIYIT5/fi_workdir/microH.dat /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/fi_workdir/microH.dat /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.o4DreIYIT5 --json_outfile /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00163_B23WHTKLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.o4DreIYIT5 --json_outfile /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00163_B23WHTKLT4_2
Running: touch /tmp/nxf.o4DreIYIT5/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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00163_B23WHTKLT4_2 --html_output /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.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.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00163_B23WHTKLT4_2 --html_output /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [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 [ENSG00000268981.5]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.o4DreIYIT5/ctat_genome_lib_build_dir > /tmp/nxf.o4DreIYIT5/tih_rna_sample_00163_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.o4DreIYIT5/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory