Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/6aefe94bc2ec209645e1d75e403e5f/tih_rna_sample_00136_B23WHTKLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/6aefe94bc2ec209645e1d75e403e5f/tih_rna_sample_00136_B23WHTKLT4_1_2.fastp.fastq.gz
  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/a8/0d9f6795574e7b31cdb296a7530afc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/0d9f6795574e7b31cdb296a7530afc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/f12ace110a8749b23de023d400ac05/tih_rna_sample_00136_B23WHTKLT4_1.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_00136_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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_00136_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf > /tmp/nxf.LHmdQCES1p/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf > /tmp/nxf.LHmdQCES1p/cytoBand.txt
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00136_B23WHTKLT4_1.star --out_dir /tmp/nxf.LHmdQCES1p/fi_workdir --reads "/tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:55:16 ..... started STAR run
Jun 08 09:55:16 ..... loading genome
Jun 08 09:57:04 ... generating Suffix Array index
Jun 08 10:00:58 ... completed Suffix Array index
Jun 08 10:00:58 ..... processing annotations GTF
Jun 08 10:00:58 ..... inserting junctions into the genome indices
Jun 08 10:02:00 ..... started mapping
Jun 08 11:10:40 ..... finished mapping
Jun 08 11:10:41 ..... started sorting BAM
Jun 08 11:10:43 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00136_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00136_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 75.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00136_B23WHTKLT4_1.star --out_dir /tmp/nxf.LHmdQCES1p/fi_workdir --reads "/tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:10:58 : INFO : Done.
Execution Time = 0.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[2330000]   -done parsing /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 120,
          ' ** passed ** ' => 9673,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 97,
          'seq-similar region overlap' => 71,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 394,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
          'excessive soft clipping' => 14528,
          'small anchor length' => 2,
          'num genes matched < 2' => 18,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
          'per_id < 96' => 9963,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 413
        };
-writing fusion junction support info.
Execution Time = 1.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[7000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[159000]   -fusion SPANNING read extraction for scaff: ACIN1--SLC7A8

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[25000]   
[26000]   -fusion SPANNING read extraction for scaff: ARHGEF10L--ACTL8

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[178000]   
[179000]   -fusion SPANNING read extraction for scaff: BAZ2B--CRTC1

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[320000]   
[321000]   -fusion SPANNING read extraction for scaff: BPNT2--KMT2C

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[90000]   
[91000]   -fusion SPANNING read extraction for scaff: CYB5RL--SSBP3

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[61000]   
[62000]   -fusion SPANNING read extraction for scaff: FGFR2--SORBS1

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[68000]   -fusion SPANNING read extraction for scaff: IARS1--NOL8

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[150000]   -fusion SPANNING read extraction for scaff: MDN1--BACH2

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[28000]   
[29000]   -fusion SPANNING read extraction for scaff: MFSD6--PMS1

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[124000]   -fusion SPANNING read extraction for scaff: NCOA6--TRPC4AP

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[55000]   -fusion SPANNING read extraction for scaff: NMNAT3--AC046134.2

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[12000]   -fusion SPANNING read extraction for scaff: NMNAT3--AC016933.1

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[89000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

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[8000]   -fusion SPANNING read extraction for scaff: OSBPL11--EGFEM1P

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[23000]   -fusion SPANNING read extraction for scaff: PAWR--PPFIA2

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

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[27000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

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[20000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

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[44000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

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[20000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

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

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[159000]   -fusion SPANNING read extraction for scaff: PSMA7--LAMA5

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[261000]   -fusion SPANNING read extraction for scaff: RERE--MTOR

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[73000]   -fusion SPANNING read extraction for scaff: SLC2A11--SMARCB1

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[26000]   -fusion SPANNING read extraction for scaff: SLC37A1--ABCG1

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[62000]   -fusion SPANNING read extraction for scaff: SORBS1--FGFR2

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[25000]   -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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[41000]   -fusion SPANNING read extraction for scaff: TRAPPC10--AGPAT3

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[39000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 68910,
          'seq similar region alignment' => 13725
        };
Execution Time = 3.84 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6666.431189
EM: Round [1] log likelihood: -6665.796984
EM: Round [2] log likelihood: -6665.777879
EM: Round [3] log likelihood: -6665.759541
EM: Round [4] log likelihood: -6665.741341
EM: Round [5] log likelihood: -6665.723266
EM: Round [6] log likelihood: -6665.705310
EM: Round [7] log likelihood: -6665.687465
EM: Round [8] log likelihood: -6665.669728
EM: Round [9] log likelihood: -6665.652092
EM: Round [10] log likelihood: -6665.634554
EM: Round [11] log likelihood: -6665.617110
EM: Round [12] log likelihood: -6665.599756
EM: Round [13] log likelihood: -6665.582490
EM: Round [14] log likelihood: -6665.565309
EM: Round [15] log likelihood: -6665.548211
EM: Round [16] log likelihood: -6665.531194
EM: Round [17] log likelihood: -6665.514257
EM: Round [18] log likelihood: -6665.497398
EM: Round [19] log likelihood: -6665.480617
EM: Round [20] log likelihood: -6665.463912
EM: Round [21] log likelihood: -6665.447284
EM: Round [22] log likelihood: -6665.430732
EM: Round [23] log likelihood: -6665.414257
EM: Round [24] log likelihood: -6665.397858
EM: Round [25] log likelihood: -6665.381536
EM: Round [26] log likelihood: -6665.365291
EM: Round [27] log likelihood: -6665.349124
EM: Round [28] log likelihood: -6665.333036
EM: Round [29] log likelihood: -6665.317028
EM: Round [30] log likelihood: -6665.301100
EM: Round [31] log likelihood: -6665.285254
EM: Round [32] log likelihood: -6665.269491
EM: Round [33] log likelihood: -6665.253811
EM: Round [34] log likelihood: -6665.238217
EM: Round [35] log likelihood: -6665.222710
EM: Round [36] log likelihood: -6665.207289
EM: Round [37] log likelihood: -6665.191958
EM: Round [38] log likelihood: -6665.176717
EM: Round [39] log likelihood: -6665.161568
EM: Round [40] log likelihood: -6665.146512
EM: Round [41] log likelihood: -6665.131549
EM: Round [42] log likelihood: -6665.116683
EM: Round [43] log likelihood: -6665.101912
EM: Round [44] log likelihood: -6665.087240
EM: Round [45] log likelihood: -6665.072667
EM: Round [46] log likelihood: -6665.058194
EM: Round [47] log likelihood: -6665.043822
EM: Round [48] log likelihood: -6665.029553
EM: Round [49] log likelihood: -6665.015388
EM: Round [50] log likelihood: -6665.001327
EM: Round [51] log likelihood: -6664.987371
EM: Round [52] log likelihood: -6664.973522
EM: Round [53] log likelihood: -6664.959779
EM: Round [54] log likelihood: -6664.946145
EM: Round [55] log likelihood: -6664.932619
EM: Round [56] log likelihood: -6664.919203
EM: Round [57] log likelihood: -6664.905896
EM: Round [58] log likelihood: -6664.892700
EM: Round [59] log likelihood: -6664.879615
EM: Round [60] log likelihood: -6664.866641
EM: Round [61] log likelihood: -6664.853779
EM: Round [62] log likelihood: -6664.841029
EM: Round [63] log likelihood: -6664.828392
EM: Round [64] log likelihood: -6664.815867
EM: Round [65] log likelihood: -6664.803455
EM: Round [66] log likelihood: -6664.791155
EM: Round [67] log likelihood: -6664.778969
EM: Round [68] log likelihood: -6664.766896
EM: Round [69] log likelihood: -6664.754935
EM: Round [70] log likelihood: -6664.743087
EM: Round [71] log likelihood: -6664.731352
EM: Round [72] log likelihood: -6664.719730
EM: Round [73] log likelihood: -6664.708219
EM: Round [74] log likelihood: -6664.696821
EM: Round [75] log likelihood: -6664.685534
EM: Round [76] log likelihood: -6664.674358
EM: Round [77] log likelihood: -6664.663293
EM: Round [78] log likelihood: -6664.652339
EM: Round [79] log likelihood: -6664.641495
EM: Round [80] log likelihood: -6664.630760
EM: Round [81] log likelihood: -6664.620134
EM: Round [82] log likelihood: -6664.609616
EM: Round [83] log likelihood: -6664.599206
EM: Round [84] log likelihood: -6664.588903
EM: Round [85] log likelihood: -6664.578706
EM: Round [86] log likelihood: -6664.568615
EM: Round [87] log likelihood: -6664.558629
EM: Round [88] log likelihood: -6664.548747
EM: Round [89] log likelihood: -6664.538969
EM: Round [90] log likelihood: -6664.529293
EM: Round [91] log likelihood: -6664.519720
EM: Round [92] log likelihood: -6664.510247
EM: Round [93] log likelihood: -6664.500875
EM: Round [94] log likelihood: -6664.491602
EM: Round [95] log likelihood: -6664.482427
EM: Round [96] log likelihood: -6664.473350
EM: Round [97] log likelihood: -6664.464370
EM: Round [98] log likelihood: -6664.455486
EM: Round [99] log likelihood: -6664.446697
EM: Round [100] log likelihood: -6664.438001
EM: Round [101] log likelihood: -6664.429399
EM: Round [102] log likelihood: -6664.420888
EM: Round [103] log likelihood: -6664.412469
EM: Round [104] log likelihood: -6664.404140
EM: Round [105] log likelihood: -6664.395901
EM: Round [106] log likelihood: -6664.387749
EM: Round [107] log likelihood: -6664.379685
EM: Round [108] log likelihood: -6664.371708
EM: Round [109] log likelihood: -6664.363815
EM: Round [110] log likelihood: -6664.356007
EM: Round [111] log likelihood: -6664.348283
EM: Round [112] log likelihood: -6664.340641
EM: Round [113] log likelihood: -6664.333080
EM: Round [114] log likelihood: -6664.325600
EM: Round [115] log likelihood: -6664.318200
EM: Round [116] log likelihood: -6664.310878
EM: Round [117] log likelihood: -6664.303634
EM: Round [118] log likelihood: -6664.296466
EM: Round [119] log likelihood: -6664.289375
EM: Round [120] log likelihood: -6664.282358
EM: Round [121] log likelihood: -6664.275415
EM: Round [122] log likelihood: -6664.268544
EM: Round [123] log likelihood: -6664.261746
EM: Round [124] log likelihood: -6664.255019
EM: Round [125] log likelihood: -6664.248362
EM: Round [126] log likelihood: -6664.241774
EM: Round [127] log likelihood: -6664.235255
EM: Round [128] log likelihood: -6664.228803
EM: Round [129] log likelihood: -6664.222418
EM: Round [130] log likelihood: -6664.216098
EM: Round [131] log likelihood: -6664.209843
EM: Round [132] log likelihood: -6664.203652
EM: Round [133] log likelihood: -6664.197524
EM: Round [134] log likelihood: -6664.191459
EM: Round [135] log likelihood: -6664.185454
EM: Round [136] log likelihood: -6664.179511
EM: Round [137] log likelihood: -6664.173627
EM: Round [138] log likelihood: -6664.167801
EM: Round [139] log likelihood: -6664.162034
EM: Round [140] log likelihood: -6664.156325
EM: Round [141] log likelihood: -6664.150672
EM: Round [142] log likelihood: -6664.145074
EM: Round [143] log likelihood: -6664.139532
EM: Round [144] log likelihood: -6664.134044
EM: Round [145] log likelihood: -6664.128609
EM: Round [146] log likelihood: -6664.123227
EM: Round [147] log likelihood: -6664.117897
EM: Round [148] log likelihood: -6664.112619
EM: Round [149] log likelihood: -6664.107391
EM: Round [150] log likelihood: -6664.102212
EM: Round [151] log likelihood: -6664.097083
EM: Round [152] log likelihood: -6664.092003
EM: Round [153] log likelihood: -6664.086970
EM: Round [154] log likelihood: -6664.081985
EM: Round [155] log likelihood: -6664.077046
EM: Round [156] log likelihood: -6664.072153
EM: Round [157] log likelihood: -6664.067305
EM: Round [158] log likelihood: -6664.062501
EM: Round [159] log likelihood: -6664.057742
EM: Round [160] log likelihood: -6664.053026
EM: Round [161] log likelihood: -6664.048353
EM: Round [162] log likelihood: -6664.043722
EM: Round [163] log likelihood: -6664.039132
EM: Round [164] log likelihood: -6664.034584
EM: Round [165] log likelihood: -6664.030075
EM: Round [166] log likelihood: -6664.025607
EM: Round [167] log likelihood: -6664.021179
EM: Round [168] log likelihood: -6664.016788
EM: Round [169] log likelihood: -6664.012437
EM: Round [170] log likelihood: -6664.008123
EM: Round [171] log likelihood: -6664.003846
EM: Round [172] log likelihood: -6663.999606
EM: Round [173] log likelihood: -6663.995402
EM: Round [174] log likelihood: -6663.991234
EM: Round [175] log likelihood: -6663.987101
EM: Round [176] log likelihood: -6663.983003
EM: Round [177] log likelihood: -6663.978939
EM: Round [178] log likelihood: -6663.974909
EM: Round [179] log likelihood: -6663.970912
EM: Round [180] log likelihood: -6663.966949
EM: Round [181] log likelihood: -6663.963017
EM: Round [182] log likelihood: -6663.959118
EM: Round [183] log likelihood: -6663.955251
EM: Round [184] log likelihood: -6663.951414
EM: Round [185] log likelihood: -6663.947609
EM: Round [186] log likelihood: -6663.943834
EM: Round [187] log likelihood: -6663.940088
EM: Round [188] log likelihood: -6663.936373
EM: Round [189] log likelihood: -6663.932686
EM: Round [190] log likelihood: -6663.929029
EM: Round [191] log likelihood: -6663.925400
EM: Round [192] log likelihood: -6663.921799
EM: Round [193] log likelihood: -6663.918226
EM: Round [194] log likelihood: -6663.914680
EM: Round [195] log likelihood: -6663.911161
EM: Round [196] log likelihood: -6663.907669
EM: Round [197] log likelihood: -6663.904203
EM: Round [198] log likelihood: -6663.900763
EM: Round [199] log likelihood: -6663.897349
EM: Round [200] log likelihood: -6663.893961
EM: Round [201] log likelihood: -6663.890597
EM: Round [202] log likelihood: -6663.887258
EM: Round [203] log likelihood: -6663.883944
EM: Round [204] log likelihood: -6663.880653
EM: Round [205] log likelihood: -6663.877387
EM: Round [206] log likelihood: -6663.874144
EM: Round [207] log likelihood: -6663.870924
EM: Round [208] log likelihood: -6663.867727
EM: Round [209] log likelihood: -6663.864553
EM: Round [210] log likelihood: -6663.861402
EM: Round [211] log likelihood: -6663.858272
EM: Round [212] log likelihood: -6663.855164
EM: Round [213] log likelihood: -6663.852079
EM: Round [214] log likelihood: -6663.849014
EM: Round [215] log likelihood: -6663.845971
EM: Round [216] log likelihood: -6663.842948
EM: Round [217] log likelihood: -6663.839946
EM: Round [218] log likelihood: -6663.836965
EM: Round [219] log likelihood: -6663.834003
EM: Round [220] log likelihood: -6663.831062
EM: Round [221] log likelihood: -6663.828140
EM: Round [222] log likelihood: -6663.825238
EM: Round [223] log likelihood: -6663.822355
EM: Round [224] log likelihood: -6663.819491
EM: Round [225] log likelihood: -6663.816646
EM: Round [226] log likelihood: -6663.813820
EM: Round [227] log likelihood: -6663.811012
EM: Round [228] log likelihood: -6663.808222
EM: Round [229] log likelihood: -6663.805450
EM: Round [230] log likelihood: -6663.802697
EM: Round [231] log likelihood: -6663.799960
EM: Round [232] log likelihood: -6663.797241
EM: Round [233] log likelihood: -6663.794540
EM: Round [234] log likelihood: -6663.791855
EM: Round [235] log likelihood: -6663.789188
EM: Round [236] log likelihood: -6663.786537
EM: Round [237] log likelihood: -6663.783903
EM: Round [238] log likelihood: -6663.781285
EM: Round [239] log likelihood: -6663.778683
EM: Round [240] log likelihood: -6663.776097
EM: Round [241] log likelihood: -6663.773527
EM: Round [242] log likelihood: -6663.770973
EM: Round [243] log likelihood: -6663.768434
EM: Round [244] log likelihood: -6663.765911
EM: Round [245] log likelihood: -6663.763403
EM: Round [246] log likelihood: -6663.760910
EM: Round [247] log likelihood: -6663.758432
EM: Round [248] log likelihood: -6663.755968
EM: Round [249] log likelihood: -6663.753520
EM: Round [250] log likelihood: -6663.751086
EM: Round [251] log likelihood: -6663.748666
EM: Round [252] log likelihood: -6663.746260
EM: Round [253] log likelihood: -6663.743869
EM: Round [254] log likelihood: -6663.741491
EM: Round [255] log likelihood: -6663.739127
EM: Round [256] log likelihood: -6663.736777
EM: Round [257] log likelihood: -6663.734440
EM: Round [258] log likelihood: -6663.732117
EM: Round [259] log likelihood: -6663.729807
EM: Round [260] log likelihood: -6663.727511
EM: Round [261] log likelihood: -6663.725227
EM: Round [262] log likelihood: -6663.722956
EM: Round [263] log likelihood: -6663.720698
EM: Round [264] log likelihood: -6663.718453
EM: Round [265] log likelihood: -6663.716220
EM: Round [266] log likelihood: -6663.714000
EM: Round [267] log likelihood: -6663.711792
EM: Round [268] log likelihood: -6663.709596
EM: Round [269] log likelihood: -6663.707413
EM: Round [270] log likelihood: -6663.705241
EM: Round [271] log likelihood: -6663.703082
EM: Round [272] log likelihood: -6663.700934
EM: Round [273] log likelihood: -6663.698798
EM: Round [274] log likelihood: -6663.696674
EM: Round [275] log likelihood: -6663.694561
EM: Round [276] log likelihood: -6663.692459
EM: Round [277] log likelihood: -6663.690369
EM: Round [278] log likelihood: -6663.688290
EM: Round [279] log likelihood: -6663.686222
EM: Round [280] log likelihood: -6663.684165
EM: Round [281] log likelihood: -6663.682119
EM: Round [282] log likelihood: -6663.680084
EM: Round [283] log likelihood: -6663.678060
EM: Round [284] log likelihood: -6663.676046
EM: Round [285] log likelihood: -6663.674043
EM: Round [286] log likelihood: -6663.672051
EM: Round [287] log likelihood: -6663.670069
EM: Round [288] log likelihood: -6663.668097
EM: Round [289] log likelihood: -6663.666135
EM: Round [290] log likelihood: -6663.664184
EM: Round [291] log likelihood: -6663.662243
EM: Round [292] log likelihood: -6663.660311
EM: Round [293] log likelihood: -6663.658390
EM: Round [294] log likelihood: -6663.656478
EM: Round [295] log likelihood: -6663.654576
EM: Round [296] log likelihood: -6663.652684
EM: Round [297] log likelihood: -6663.650802
EM: Round [298] log likelihood: -6663.648929
EM: Round [299] log likelihood: -6663.647066
EM: Round [300] log likelihood: -6663.645211
EM: Round [301] log likelihood: -6663.643367
EM: Round [302] log likelihood: -6663.641531
EM: Round [303] log likelihood: -6663.639705
EM: Round [304] log likelihood: -6663.637888
EM: Round [305] log likelihood: -6663.636080
EM: Round [306] log likelihood: -6663.634280
EM: Round [307] log likelihood: -6663.632490
EM: Round [308] log likelihood: -6663.630709
EM: Round [309] log likelihood: -6663.628936
EM: Round [310] log likelihood: -6663.627172
EM: Round [311] log likelihood: -6663.625417
EM: Round [312] log likelihood: -6663.623671
EM: Round [313] log likelihood: -6663.621932
EM: Round [314] log likelihood: -6663.620203
EM: Round [315] log likelihood: -6663.618482
EM: Round [316] log likelihood: -6663.616769
EM: Round [317] log likelihood: -6663.615064
EM: Round [318] log likelihood: -6663.613368
EM: Round [319] log likelihood: -6663.611680
EM: Round [320] log likelihood: -6663.610000
EM: Round [321] log likelihood: -6663.608328
EM: Round [322] log likelihood: -6663.606664
EM: Round [323] log likelihood: -6663.605008
EM: Round [324] log likelihood: -6663.603360
EM: Round [325] log likelihood: -6663.601719
EM: Round [326] log likelihood: -6663.600087
EM: Round [327] log likelihood: -6663.598462
EM: Round [328] log likelihood: -6663.596845
EM: Round [329] log likelihood: -6663.595236
EM: Round [330] log likelihood: -6663.593634
EM: Round [331] log likelihood: -6663.592039
EM: Round [332] log likelihood: -6663.590452
EM: Round [333] log likelihood: -6663.588873
EM: Round [334] log likelihood: -6663.587301
EM: Round [335] log likelihood: -6663.585736
EM: Round [336] log likelihood: -6663.584179
EM: Round [337] log likelihood: -6663.582629
EM: Round [338] log likelihood: -6663.581086
EM: Round [339] log likelihood: -6663.579550
EM: Round [340] log likelihood: -6663.578021
EM: Round [341] log likelihood: -6663.576499
EM: Round [342] log likelihood: -6663.574984
EM: Round [343] log likelihood: -6663.573477
EM: Round [344] log likelihood: -6663.571976
EM: Round [345] log likelihood: -6663.570482
EM: Round [346] log likelihood: -6663.568995
EM: Round [347] log likelihood: -6663.567514
EM: Round [348] log likelihood: -6663.566040
EM: Round [349] log likelihood: -6663.564573
EM: Round [350] log likelihood: -6663.563113
EM: Round [351] log likelihood: -6663.561659
EM: Round [352] log likelihood: -6663.560212
EM: Round [353] log likelihood: -6663.558772
EM: Round [354] log likelihood: -6663.557338
EM: Round [355] log likelihood: -6663.555910
EM: Round [356] log likelihood: -6663.554489
EM: Round [357] log likelihood: -6663.553074
EM: Round [358] log likelihood: -6663.551665
EM: Round [359] log likelihood: -6663.550263
EM: Round [360] log likelihood: -6663.548867
EM: Round [361] log likelihood: -6663.547477
EM: Round [362] log likelihood: -6663.546094
EM: Round [363] log likelihood: -6663.544716
EM: Round [364] log likelihood: -6663.543345
EM: Round [365] log likelihood: -6663.541979
EM: Round [366] log likelihood: -6663.540620
EM: Round [367] log likelihood: -6663.539267
EM: Round [368] log likelihood: -6663.537919
EM: Round [369] log likelihood: -6663.536578
EM: Round [370] log likelihood: -6663.535243
EM: Round [371] log likelihood: -6663.533913
EM: Round [372] log likelihood: -6663.532589
EM: Round [373] log likelihood: -6663.531271
EM: Round [374] log likelihood: -6663.529959
EM: Round [375] log likelihood: -6663.528652
EM: Round [376] log likelihood: -6663.527351
EM: Round [377] log likelihood: -6663.526056
EM: Round [378] log likelihood: -6663.524766
EM: Round [379] log likelihood: -6663.523482
EM: Round [380] log likelihood: -6663.522204
EM: Round [381] log likelihood: -6663.520931
EM: Round [382] log likelihood: -6663.519663
EM: Round [383] log likelihood: -6663.518401
EM: Round [384] log likelihood: -6663.517145
EM: Round [385] log likelihood: -6663.515893
EM: Round [386] log likelihood: -6663.514648
EM: Round [387] log likelihood: -6663.513407
EM: Round [388] log likelihood: -6663.512172
EM: Round [389] log likelihood: -6663.510942
EM: Round [390] log likelihood: -6663.509717
EM: Round [391] log likelihood: -6663.508498
EM: Round [392] log likelihood: -6663.507284
EM: Round [393] log likelihood: -6663.506075
EM: Round [394] log likelihood: -6663.504871
EM: Round [395] log likelihood: -6663.503672
EM: Round [396] log likelihood: -6663.502478
EM: Round [397] log likelihood: -6663.501289
EM: Round [398] log likelihood: -6663.500105
EM: Round [399] log likelihood: -6663.498927
EM: Round [400] log likelihood: -6663.497753
EM: Round [401] log likelihood: -6663.496584
EM: Round [402] log likelihood: -6663.495420
EM: Round [403] log likelihood: -6663.494261
EM: Round [404] log likelihood: -6663.493107
EM: Round [405] log likelihood: -6663.491958
EM: Round [406] log likelihood: -6663.490813
EM: Round [407] log likelihood: -6663.489673
EM: Round [408] log likelihood: -6663.488538
EM: Round [409] log likelihood: -6663.487408
EM: Round [410] log likelihood: -6663.486282
EM: Round [411] log likelihood: -6663.485161
EM: Round [412] log likelihood: -6663.484045
EM: Round [413] log likelihood: -6663.482933
EM: Round [414] log likelihood: -6663.481826
EM: Round [415] log likelihood: -6663.480724
EM: Round [416] log likelihood: -6663.479626
EM: Round [417] log likelihood: -6663.478533
EM: Round [418] log likelihood: -6663.477444
EM: Round [419] log likelihood: -6663.476359
EM: Round [420] log likelihood: -6663.475279
EM: Round [421] log likelihood: -6663.474204
EM: Round [422] log likelihood: -6663.473133
EM: Round [423] log likelihood: -6663.472066
EM: Round [424] log likelihood: -6663.471004
EM: Round [425] log likelihood: -6663.469946
EM: Round [426] log likelihood: -6663.468892
EM: Round [427] log likelihood: -6663.467842
EM: Round [428] log likelihood: -6663.466797
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EM: Round [885] log likelihood: -6663.237153
EM: Round [886] log likelihood: -6663.236946
EM: Round [887] log likelihood: -6663.236739
EM: Round [888] log likelihood: -6663.236533
EM: Round [889] log likelihood: -6663.236327
EM: Round [890] log likelihood: -6663.236122
EM: Round [891] log likelihood: -6663.235918
EM: Round [892] log likelihood: -6663.235714
EM: Round [893] log likelihood: -6663.235511
EM: Round [894] log likelihood: -6663.235309
EM: Round [895] log likelihood: -6663.235107
EM: Round [896] log likelihood: -6663.234906
EM: Round [897] log likelihood: -6663.234706
EM: Round [898] log likelihood: -6663.234506
EM: Round [899] log likelihood: -6663.234307
EM: Round [900] log likelihood: -6663.234109
EM: Round [901] log likelihood: -6663.233911
EM: Round [902] log likelihood: -6663.233714
EM: Round [903] log likelihood: -6663.233518
EM: Round [904] log likelihood: -6663.233322
EM: Round [905] log likelihood: -6663.233126
EM: Round [906] log likelihood: -6663.232932
EM: Round [907] log likelihood: -6663.232738
EM: Round [908] log likelihood: -6663.232545
EM: Round [909] log likelihood: -6663.232352
EM: Round [910] log likelihood: -6663.232160
EM: Round [911] log likelihood: -6663.231968
EM: Round [912] log likelihood: -6663.231777
EM: Round [913] log likelihood: -6663.231587
EM: Round [914] log likelihood: -6663.231397
EM: Round [915] log likelihood: -6663.231208
EM: Round [916] log likelihood: -6663.231020
EM: Round [917] log likelihood: -6663.230832
EM: Round [918] log likelihood: -6663.230645
EM: Round [919] log likelihood: -6663.230458
EM: Round [920] log likelihood: -6663.230272
EM: Round [921] log likelihood: -6663.230087
EM: Round [922] log likelihood: -6663.229902
EM: Round [923] log likelihood: -6663.229718
EM: Round [924] log likelihood: -6663.229534
EM: Round [925] log likelihood: -6663.229351
EM: Round [926] log likelihood: -6663.229168
EM: Round [927] log likelihood: -6663.228986
EM: Round [928] log likelihood: -6663.228805
EM: Round [929] log likelihood: -6663.228624
EM: Round [930] log likelihood: -6663.228444
EM: Round [931] log likelihood: -6663.228265
EM: Round [932] log likelihood: -6663.228086
EM: Round [933] log likelihood: -6663.227907
EM: Round [934] log likelihood: -6663.227729
EM: Round [935] log likelihood: -6663.227552
EM: Round [936] log likelihood: -6663.227375
EM: Round [937] log likelihood: -6663.227199
EM: Round [938] log likelihood: -6663.227024
EM: Round [939] log likelihood: -6663.226849
EM: Round [940] log likelihood: -6663.226674
EM: Round [941] log likelihood: -6663.226500
EM: Round [942] log likelihood: -6663.226327
EM: Round [943] log likelihood: -6663.226154
EM: Round [944] log likelihood: -6663.225982
EM: Round [945] log likelihood: -6663.225810
EM: Round [946] log likelihood: -6663.225639
EM: Round [947] log likelihood: -6663.225468
EM: Round [948] log likelihood: -6663.225298
EM: Round [949] log likelihood: -6663.225129
EM: Round [950] log likelihood: -6663.224960
EM: Round [951] log likelihood: -6663.224791
EM: Round [952] log likelihood: -6663.224623
EM: Round [953] log likelihood: -6663.224456
EM: Round [954] log likelihood: -6663.224289
EM: Round [955] log likelihood: -6663.224123
EM: Round [956] log likelihood: -6663.223957
EM: Round [957] log likelihood: -6663.223792
EM: Round [958] log likelihood: -6663.223627
EM: Round [959] log likelihood: -6663.223463
EM: Round [960] log likelihood: -6663.223299
EM: Round [961] log likelihood: -6663.223136
EM: Round [962] log likelihood: -6663.222973
EM: Round [963] log likelihood: -6663.222811
EM: Round [964] log likelihood: -6663.222649
EM: Round [965] log likelihood: -6663.222488
EM: Round [966] log likelihood: -6663.222328
EM: Round [967] log likelihood: -6663.222168
EM: Round [968] log likelihood: -6663.222008
EM: Round [969] log likelihood: -6663.221849
EM: Round [970] log likelihood: -6663.221691
EM: Round [971] log likelihood: -6663.221532
EM: Round [972] log likelihood: -6663.221375
EM: Round [973] log likelihood: -6663.221218
EM: Round [974] log likelihood: -6663.221061
EM: Round [975] log likelihood: -6663.220905
EM: Round [976] log likelihood: -6663.220750
EM: Round [977] log likelihood: -6663.220595
EM: Round [978] log likelihood: -6663.220440
EM: Round [979] log likelihood: -6663.220286
EM: Round [980] log likelihood: -6663.220132
EM: Round [981] log likelihood: -6663.219979
EM: Round [982] log likelihood: -6663.219827
EM: Round [983] log likelihood: -6663.219675
EM: Round [984] log likelihood: -6663.219523
EM: Round [985] log likelihood: -6663.219372
EM: Round [986] log likelihood: -6663.219221
EM: Round [987] log likelihood: -6663.219071
EM: Round [988] log likelihood: -6663.218921
EM: Round [989] log likelihood: -6663.218772
EM: Round [990] log likelihood: -6663.218623
EM: Round [991] log likelihood: -6663.218475
EM: Round [992] log likelihood: -6663.218327
EM: Round [993] log likelihood: -6663.218180
EM: Round [994] log likelihood: -6663.218033
EM: Round [995] log likelihood: -6663.217886
EM: Round [996] log likelihood: -6663.217740
EM: Round [997] log likelihood: -6663.217595
EM: Round [998] log likelihood: -6663.217450
EM: Round [999] log likelihood: -6663.217305
EM: Round [1000] log likelihood: -6663.217161
EM: Round [1001] log likelihood: -6663.217017
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/tih_rna_sample_00136_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa > /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir
-done, see /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5241.240408
EM: Round [1] log likelihood: -5241.193040
EM: Round [2] log likelihood: -5241.192603
EM: Round [3] log likelihood: -5241.192596
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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_1.fastp.fastq.gz: 262294379
Execution Time = 5.31 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa --gtf /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf  > /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fa --gtf /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.gtf  > /tmp/nxf.LHmdQCES1p/fi_workdir/microH.dat
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.LHmdQCES1p/fi_workdir/microH.dat /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/fi_workdir/microH.dat /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.LHmdQCES1p --json_outfile /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00136_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.LHmdQCES1p --json_outfile /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00136_B23WHTKLT4_1
Running: touch /tmp/nxf.LHmdQCES1p/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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00136_B23WHTKLT4_1 --html_output /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_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.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00136_B23WHTKLT4_1 --html_output /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000206120.11]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.LHmdQCES1p/ctat_genome_lib_build_dir > /tmp/nxf.LHmdQCES1p/tih_rna_sample_00136_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.LHmdQCES1p/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory