Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/d54225ddd6737e14791fcfb7249325/659_bNS-T1-TRNA-1_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/00/2007b29c08245fae1591d03403d00d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/2007b29c08245fae1591d03403d00d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/d54225ddd6737e14791fcfb7249325/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/2cb56d52c9912f948e8d67c400308d/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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 659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/cytoBand.txt
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.sA3rneZbym/fi_workdir --reads "/tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:22:41 ..... started STAR run
Jun 08 10:22:41 ..... loading genome
Jun 08 10:24:33 ... generating Suffix Array index
Jun 08 10:28:55 ... completed Suffix Array index
Jun 08 10:28:55 ..... processing annotations GTF
Jun 08 10:28:55 ..... inserting junctions into the genome indices
Jun 08 10:30:06 ..... started mapping
Jun 08 11:35:42 ..... finished mapping
Jun 08 11:35:44 ..... started sorting BAM
Jun 08 11:35:44 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 73.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.sA3rneZbym/fi_workdir --reads "/tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:35:47 : INFO : Done.
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[370000]   -done parsing /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 1247,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2,
          'num genes matched < 2' => 4,
          'small anchor length' => 14,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 8,
          'excessive soft clipping' => 2609,
          ' ** passed ** ' => 9320,
          'exons hit < 2' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1
        };
-writing fusion junction support info.
Execution Time = 0.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[123000]   -fusion SPANNING read extraction for scaff: EML4--ALK

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[23000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[46000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 906,
          'seq similar region alignment' => 17068
        };
Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -1607.712150
EM: Round [1] log likelihood: -1607.672747
EM: Round [2] log likelihood: -1607.652177
EM: Round [3] log likelihood: -1607.632071
EM: Round [4] log likelihood: -1607.612408
EM: Round [5] log likelihood: -1607.593170
EM: Round [6] log likelihood: -1607.574341
EM: Round [7] log likelihood: -1607.555905
EM: Round [8] log likelihood: -1607.537845
EM: Round [9] log likelihood: -1607.520149
EM: Round [10] log likelihood: -1607.502802
EM: Round [11] log likelihood: -1607.485792
EM: Round [12] log likelihood: -1607.469106
EM: Round [13] log likelihood: -1607.452734
EM: Round [14] log likelihood: -1607.436664
EM: Round [15] log likelihood: -1607.420886
EM: Round [16] log likelihood: -1607.405390
EM: Round [17] log likelihood: -1607.390168
EM: Round [18] log likelihood: -1607.375210
EM: Round [19] log likelihood: -1607.360508
EM: Round [20] log likelihood: -1607.346054
EM: Round [21] log likelihood: -1607.331840
EM: Round [22] log likelihood: -1607.317859
EM: Round [23] log likelihood: -1607.304104
EM: Round [24] log likelihood: -1607.290568
EM: Round [25] log likelihood: -1607.277245
EM: Round [26] log likelihood: -1607.264128
EM: Round [27] log likelihood: -1607.251213
EM: Round [28] log likelihood: -1607.238493
EM: Round [29] log likelihood: -1607.225963
EM: Round [30] log likelihood: -1607.213618
EM: Round [31] log likelihood: -1607.201453
EM: Round [32] log likelihood: -1607.189463
EM: Round [33] log likelihood: -1607.177644
EM: Round [34] log likelihood: -1607.165990
EM: Round [35] log likelihood: -1607.154499
EM: Round [36] log likelihood: -1607.143166
EM: Round [37] log likelihood: -1607.131986
EM: Round [38] log likelihood: -1607.120957
EM: Round [39] log likelihood: -1607.110075
EM: Round [40] log likelihood: -1607.099335
EM: Round [41] log likelihood: -1607.088735
EM: Round [42] log likelihood: -1607.078272
EM: Round [43] log likelihood: -1607.067942
EM: Round [44] log likelihood: -1607.057742
EM: Round [45] log likelihood: -1607.047670
EM: Round [46] log likelihood: -1607.037722
EM: Round [47] log likelihood: -1607.027895
EM: Round [48] log likelihood: -1607.018188
EM: Round [49] log likelihood: -1607.008597
EM: Round [50] log likelihood: -1606.999121
EM: Round [51] log likelihood: -1606.989755
EM: Round [52] log likelihood: -1606.980500
EM: Round [53] log likelihood: -1606.971351
EM: Round [54] log likelihood: -1606.962307
EM: Round [55] log likelihood: -1606.953365
EM: Round [56] log likelihood: -1606.944524
EM: Round [57] log likelihood: -1606.935782
EM: Round [58] log likelihood: -1606.927137
EM: Round [59] log likelihood: -1606.918586
EM: Round [60] log likelihood: -1606.910128
EM: Round [61] log likelihood: -1606.901761
EM: Round [62] log likelihood: -1606.893484
EM: Round [63] log likelihood: -1606.885294
EM: Round [64] log likelihood: -1606.877191
EM: Round [65] log likelihood: -1606.869172
EM: Round [66] log likelihood: -1606.861236
EM: Round [67] log likelihood: -1606.853382
EM: Round [68] log likelihood: -1606.845607
EM: Round [69] log likelihood: -1606.837912
EM: Round [70] log likelihood: -1606.830293
EM: Round [71] log likelihood: -1606.822750
EM: Round [72] log likelihood: -1606.815282
EM: Round [73] log likelihood: -1606.807887
EM: Round [74] log likelihood: -1606.800564
EM: Round [75] log likelihood: -1606.793312
EM: Round [76] log likelihood: -1606.786129
EM: Round [77] log likelihood: -1606.779015
EM: Round [78] log likelihood: -1606.771968
EM: Round [79] log likelihood: -1606.764987
EM: Round [80] log likelihood: -1606.758071
EM: Round [81] log likelihood: -1606.751220
EM: Round [82] log likelihood: -1606.744431
EM: Round [83] log likelihood: -1606.737705
EM: Round [84] log likelihood: -1606.731040
EM: Round [85] log likelihood: -1606.724434
EM: Round [86] log likelihood: -1606.717888
EM: Round [87] log likelihood: -1606.711400
EM: Round [88] log likelihood: -1606.704970
EM: Round [89] log likelihood: -1606.698596
EM: Round [90] log likelihood: -1606.692278
EM: Round [91] log likelihood: -1606.686014
EM: Round [92] log likelihood: -1606.679805
EM: Round [93] log likelihood: -1606.673649
EM: Round [94] log likelihood: -1606.667545
EM: Round [95] log likelihood: -1606.661493
EM: Round [96] log likelihood: -1606.655492
EM: Round [97] log likelihood: -1606.649541
EM: Round [98] log likelihood: -1606.643639
EM: Round [99] log likelihood: -1606.637786
EM: Round [100] log likelihood: -1606.631982
EM: Round [101] log likelihood: -1606.626225
EM: Round [102] log likelihood: -1606.620514
EM: Round [103] log likelihood: -1606.614850
EM: Round [104] log likelihood: -1606.609231
EM: Round [105] log likelihood: -1606.603657
EM: Round [106] log likelihood: -1606.598128
EM: Round [107] log likelihood: -1606.592642
EM: Round [108] log likelihood: -1606.587199
EM: Round [109] log likelihood: -1606.581799
EM: Round [110] log likelihood: -1606.576441
EM: Round [111] log likelihood: -1606.571124
EM: Round [112] log likelihood: -1606.565848
EM: Round [113] log likelihood: -1606.560612
EM: Round [114] log likelihood: -1606.555417
EM: Round [115] log likelihood: -1606.550260
EM: Round [116] log likelihood: -1606.545143
EM: Round [117] log likelihood: -1606.540063
EM: Round [118] log likelihood: -1606.535022
EM: Round [119] log likelihood: -1606.530018
EM: Round [120] log likelihood: -1606.525051
EM: Round [121] log likelihood: -1606.520121
EM: Round [122] log likelihood: -1606.515226
EM: Round [123] log likelihood: -1606.510367
EM: Round [124] log likelihood: -1606.505544
EM: Round [125] log likelihood: -1606.500755
EM: Round [126] log likelihood: -1606.496000
EM: Round [127] log likelihood: -1606.491279
EM: Round [128] log likelihood: -1606.486592
EM: Round [129] log likelihood: -1606.481938
EM: Round [130] log likelihood: -1606.477317
EM: Round [131] log likelihood: -1606.472728
EM: Round [132] log likelihood: -1606.468171
EM: Round [133] log likelihood: -1606.463646
EM: Round [134] log likelihood: -1606.459152
EM: Round [135] log likelihood: -1606.454689
EM: Round [136] log likelihood: -1606.450257
EM: Round [137] log likelihood: -1606.445854
EM: Round [138] log likelihood: -1606.441482
EM: Round [139] log likelihood: -1606.437139
EM: Round [140] log likelihood: -1606.432825
EM: Round [141] log likelihood: -1606.428541
EM: Round [142] log likelihood: -1606.424285
EM: Round [143] log likelihood: -1606.420057
EM: Round [144] log likelihood: -1606.415857
EM: Round [145] log likelihood: -1606.411685
EM: Round [146] log likelihood: -1606.407540
EM: Round [147] log likelihood: -1606.403422
EM: Round [148] log likelihood: -1606.399331
EM: Round [149] log likelihood: -1606.395267
EM: Round [150] log likelihood: -1606.391229
EM: Round [151] log likelihood: -1606.387216
EM: Round [152] log likelihood: -1606.383230
EM: Round [153] log likelihood: -1606.379269
EM: Round [154] log likelihood: -1606.375333
EM: Round [155] log likelihood: -1606.371422
EM: Round [156] log likelihood: -1606.367535
EM: Round [157] log likelihood: -1606.363673
EM: Round [158] log likelihood: -1606.359836
EM: Round [159] log likelihood: -1606.356022
EM: Round [160] log likelihood: -1606.352231
EM: Round [161] log likelihood: -1606.348465
EM: Round [162] log likelihood: -1606.344721
EM: Round [163] log likelihood: -1606.341000
EM: Round [164] log likelihood: -1606.337303
EM: Round [165] log likelihood: -1606.333627
EM: Round [166] log likelihood: -1606.329974
EM: Round [167] log likelihood: -1606.326343
EM: Round [168] log likelihood: -1606.322734
EM: Round [169] log likelihood: -1606.319147
EM: Round [170] log likelihood: -1606.315581
EM: Round [171] log likelihood: -1606.312036
EM: Round [172] log likelihood: -1606.308512
EM: Round [173] log likelihood: -1606.305010
EM: Round [174] log likelihood: -1606.301528
EM: Round [175] log likelihood: -1606.298066
EM: Round [176] log likelihood: -1606.294625
EM: Round [177] log likelihood: -1606.291203
EM: Round [178] log likelihood: -1606.287802
EM: Round [179] log likelihood: -1606.284420
EM: Round [180] log likelihood: -1606.281058
EM: Round [181] log likelihood: -1606.277716
EM: Round [182] log likelihood: -1606.274392
EM: Round [183] log likelihood: -1606.271088
EM: Round [184] log likelihood: -1606.267802
EM: Round [185] log likelihood: -1606.264535
EM: Round [186] log likelihood: -1606.261287
EM: Round [187] log likelihood: -1606.258056
EM: Round [188] log likelihood: -1606.254845
EM: Round [189] log likelihood: -1606.251651
EM: Round [190] log likelihood: -1606.248475
EM: Round [191] log likelihood: -1606.245316
EM: Round [192] log likelihood: -1606.242175
EM: Round [193] log likelihood: -1606.239052
EM: Round [194] log likelihood: -1606.235946
EM: Round [195] log likelihood: -1606.232857
EM: Round [196] log likelihood: -1606.229785
EM: Round [197] log likelihood: -1606.226730
EM: Round [198] log likelihood: -1606.223691
EM: Round [199] log likelihood: -1606.220669
EM: Round [200] log likelihood: -1606.217663
EM: Round [201] log likelihood: -1606.214674
EM: Round [202] log likelihood: -1606.211701
EM: Round [203] log likelihood: -1606.208743
EM: Round [204] log likelihood: -1606.205802
EM: Round [205] log likelihood: -1606.202876
EM: Round [206] log likelihood: -1606.199966
EM: Round [207] log likelihood: -1606.197071
EM: Round [208] log likelihood: -1606.194192
EM: Round [209] log likelihood: -1606.191328
EM: Round [210] log likelihood: -1606.188479
EM: Round [211] log likelihood: -1606.185645
EM: Round [212] log likelihood: -1606.182825
EM: Round [213] log likelihood: -1606.180021
EM: Round [214] log likelihood: -1606.177231
EM: Round [215] log likelihood: -1606.174455
EM: Round [216] log likelihood: -1606.171694
EM: Round [217] log likelihood: -1606.168948
EM: Round [218] log likelihood: -1606.166215
EM: Round [219] log likelihood: -1606.163496
EM: Round [220] log likelihood: -1606.160792
EM: Round [221] log likelihood: -1606.158101
EM: Round [222] log likelihood: -1606.155424
EM: Round [223] log likelihood: -1606.152760
EM: Round [224] log likelihood: -1606.150110
EM: Round [225] log likelihood: -1606.147473
EM: Round [226] log likelihood: -1606.144850
EM: Round [227] log likelihood: -1606.142240
EM: Round [228] log likelihood: -1606.139643
EM: Round [229] log likelihood: -1606.137059
EM: Round [230] log likelihood: -1606.134487
EM: Round [231] log likelihood: -1606.131929
EM: Round [232] log likelihood: -1606.129383
EM: Round [233] log likelihood: -1606.126850
EM: Round [234] log likelihood: -1606.124330
EM: Round [235] log likelihood: -1606.121821
EM: Round [236] log likelihood: -1606.119326
EM: Round [237] log likelihood: -1606.116842
EM: Round [238] log likelihood: -1606.114370
EM: Round [239] log likelihood: -1606.111911
EM: Round [240] log likelihood: -1606.109464
EM: Round [241] log likelihood: -1606.107028
EM: Round [242] log likelihood: -1606.104604
EM: Round [243] log likelihood: -1606.102192
EM: Round [244] log likelihood: -1606.099792
EM: Round [245] log likelihood: -1606.097403
EM: Round [246] log likelihood: -1606.095025
EM: Round [247] log likelihood: -1606.092659
EM: Round [248] log likelihood: -1606.090305
EM: Round [249] log likelihood: -1606.087961
EM: Round [250] log likelihood: -1606.085629
EM: Round [251] log likelihood: -1606.083307
EM: Round [252] log likelihood: -1606.080997
EM: Round [253] log likelihood: -1606.078697
EM: Round [254] log likelihood: -1606.076409
EM: Round [255] log likelihood: -1606.074131
EM: Round [256] log likelihood: -1606.071864
EM: Round [257] log likelihood: -1606.069607
EM: Round [258] log likelihood: -1606.067361
EM: Round [259] log likelihood: -1606.065125
EM: Round [260] log likelihood: -1606.062900
EM: Round [261] log likelihood: -1606.060685
EM: Round [262] log likelihood: -1606.058480
EM: Round [263] log likelihood: -1606.056286
EM: Round [264] log likelihood: -1606.054101
EM: Round [265] log likelihood: -1606.051927
EM: Round [266] log likelihood: -1606.049762
EM: Round [267] log likelihood: -1606.047608
EM: Round [268] log likelihood: -1606.045463
EM: Round [269] log likelihood: -1606.043328
EM: Round [270] log likelihood: -1606.041203
EM: Round [271] log likelihood: -1606.039087
EM: Round [272] log likelihood: -1606.036981
EM: Round [273] log likelihood: -1606.034885
EM: Round [274] log likelihood: -1606.032797
EM: Round [275] log likelihood: -1606.030720
EM: Round [276] log likelihood: -1606.028651
EM: Round [277] log likelihood: -1606.026592
EM: Round [278] log likelihood: -1606.024542
EM: Round [279] log likelihood: -1606.022502
EM: Round [280] log likelihood: -1606.020470
EM: Round [281] log likelihood: -1606.018447
EM: Round [282] log likelihood: -1606.016434
EM: Round [283] log likelihood: -1606.014429
EM: Round [284] log likelihood: -1606.012433
EM: Round [285] log likelihood: -1606.010446
EM: Round [286] log likelihood: -1606.008467
EM: Round [287] log likelihood: -1606.006498
EM: Round [288] log likelihood: -1606.004536
EM: Round [289] log likelihood: -1606.002584
EM: Round [290] log likelihood: -1606.000640
EM: Round [291] log likelihood: -1605.998704
EM: Round [292] log likelihood: -1605.996777
EM: Round [293] log likelihood: -1605.994858
EM: Round [294] log likelihood: -1605.992948
EM: Round [295] log likelihood: -1605.991046
EM: Round [296] log likelihood: -1605.989152
EM: Round [297] log likelihood: -1605.987266
EM: Round [298] log likelihood: -1605.985388
EM: Round [299] log likelihood: -1605.983518
EM: Round [300] log likelihood: -1605.981657
EM: Round [301] log likelihood: -1605.979803
EM: Round [302] log likelihood: -1605.977957
EM: Round [303] log likelihood: -1605.976119
EM: Round [304] log likelihood: -1605.974289
EM: Round [305] log likelihood: -1605.972467
EM: Round [306] log likelihood: -1605.970652
EM: Round [307] log likelihood: -1605.968845
EM: Round [308] log likelihood: -1605.967046
EM: Round [309] log likelihood: -1605.965254
EM: Round [310] log likelihood: -1605.963470
EM: Round [311] log likelihood: -1605.961693
EM: Round [312] log likelihood: -1605.959923
EM: Round [313] log likelihood: -1605.958161
EM: Round [314] log likelihood: -1605.956407
EM: Round [315] log likelihood: -1605.954660
EM: Round [316] log likelihood: -1605.952920
EM: Round [317] log likelihood: -1605.951187
EM: Round [318] log likelihood: -1605.949461
EM: Round [319] log likelihood: -1605.947743
EM: Round [320] log likelihood: -1605.946031
EM: Round [321] log likelihood: -1605.944327
EM: Round [322] log likelihood: -1605.942630
EM: Round [323] log likelihood: -1605.940939
EM: Round [324] log likelihood: -1605.939256
EM: Round [325] log likelihood: -1605.937579
EM: Round [326] log likelihood: -1605.935910
EM: Round [327] log likelihood: -1605.934247
EM: Round [328] log likelihood: -1605.932591
EM: Round [329] log likelihood: -1605.930942
EM: Round [330] log likelihood: -1605.929299
EM: Round [331] log likelihood: -1605.927663
EM: Round [332] log likelihood: -1605.926034
EM: Round [333] log likelihood: -1605.924411
EM: Round [334] log likelihood: -1605.922795
EM: Round [335] log likelihood: -1605.921185
EM: Round [336] log likelihood: -1605.919582
EM: Round [337] log likelihood: -1605.917985
EM: Round [338] log likelihood: -1605.916395
EM: Round [339] log likelihood: -1605.914811
EM: Round [340] log likelihood: -1605.913233
EM: Round [341] log likelihood: -1605.911662
EM: Round [342] log likelihood: -1605.910097
EM: Round [343] log likelihood: -1605.908538
EM: Round [344] log likelihood: -1605.906985
EM: Round [345] log likelihood: -1605.905439
EM: Round [346] log likelihood: -1605.903898
EM: Round [347] log likelihood: -1605.902364
EM: Round [348] log likelihood: -1605.900836
EM: Round [349] log likelihood: -1605.899313
EM: Round [350] log likelihood: -1605.897797
EM: Round [351] log likelihood: -1605.896287
EM: Round [352] log likelihood: -1605.894783
EM: Round [353] log likelihood: -1605.893284
EM: Round [354] log likelihood: -1605.891792
EM: Round [355] log likelihood: -1605.890305
EM: Round [356] log likelihood: -1605.888824
EM: Round [357] log likelihood: -1605.887349
EM: Round [358] log likelihood: -1605.885879
EM: Round [359] log likelihood: -1605.884415
EM: Round [360] log likelihood: -1605.882957
EM: Round [361] log likelihood: -1605.881505
EM: Round [362] log likelihood: -1605.880058
EM: Round [363] log likelihood: -1605.878617
EM: Round [364] log likelihood: -1605.877181
EM: Round [365] log likelihood: -1605.875751
EM: Round [366] log likelihood: -1605.874326
EM: Round [367] log likelihood: -1605.872907
EM: Round [368] log likelihood: -1605.871493
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EM: Round [826] log likelihood: -1605.541988
EM: Round [827] log likelihood: -1605.541654
EM: Round [828] log likelihood: -1605.541321
EM: Round [829] log likelihood: -1605.540989
EM: Round [830] log likelihood: -1605.540658
EM: Round [831] log likelihood: -1605.540328
EM: Round [832] log likelihood: -1605.539998
EM: Round [833] log likelihood: -1605.539670
EM: Round [834] log likelihood: -1605.539342
EM: Round [835] log likelihood: -1605.539016
EM: Round [836] log likelihood: -1605.538690
EM: Round [837] log likelihood: -1605.538365
EM: Round [838] log likelihood: -1605.538041
EM: Round [839] log likelihood: -1605.537718
EM: Round [840] log likelihood: -1605.537396
EM: Round [841] log likelihood: -1605.537075
EM: Round [842] log likelihood: -1605.536754
EM: Round [843] log likelihood: -1605.536435
EM: Round [844] log likelihood: -1605.536116
EM: Round [845] log likelihood: -1605.535799
EM: Round [846] log likelihood: -1605.535482
EM: Round [847] log likelihood: -1605.535166
EM: Round [848] log likelihood: -1605.534850
EM: Round [849] log likelihood: -1605.534536
EM: Round [850] log likelihood: -1605.534223
EM: Round [851] log likelihood: -1605.533910
EM: Round [852] log likelihood: -1605.533598
EM: Round [853] log likelihood: -1605.533287
EM: Round [854] log likelihood: -1605.532977
EM: Round [855] log likelihood: -1605.532668
EM: Round [856] log likelihood: -1605.532360
EM: Round [857] log likelihood: -1605.532052
EM: Round [858] log likelihood: -1605.531746
EM: Round [859] log likelihood: -1605.531440
EM: Round [860] log likelihood: -1605.531135
EM: Round [861] log likelihood: -1605.530831
EM: Round [862] log likelihood: -1605.530527
EM: Round [863] log likelihood: -1605.530225
EM: Round [864] log likelihood: -1605.529923
EM: Round [865] log likelihood: -1605.529622
EM: Round [866] log likelihood: -1605.529322
EM: Round [867] log likelihood: -1605.529023
EM: Round [868] log likelihood: -1605.528725
EM: Round [869] log likelihood: -1605.528427
EM: Round [870] log likelihood: -1605.528130
EM: Round [871] log likelihood: -1605.527834
EM: Round [872] log likelihood: -1605.527539
EM: Round [873] log likelihood: -1605.527245
EM: Round [874] log likelihood: -1605.526951
EM: Round [875] log likelihood: -1605.526658
EM: Round [876] log likelihood: -1605.526366
EM: Round [877] log likelihood: -1605.526075
EM: Round [878] log likelihood: -1605.525785
EM: Round [879] log likelihood: -1605.525495
EM: Round [880] log likelihood: -1605.525206
EM: Round [881] log likelihood: -1605.524918
EM: Round [882] log likelihood: -1605.524631
EM: Round [883] log likelihood: -1605.524344
EM: Round [884] log likelihood: -1605.524059
EM: Round [885] log likelihood: -1605.523774
EM: Round [886] log likelihood: -1605.523490
EM: Round [887] log likelihood: -1605.523206
EM: Round [888] log likelihood: -1605.522923
EM: Round [889] log likelihood: -1605.522642
EM: Round [890] log likelihood: -1605.522360
EM: Round [891] log likelihood: -1605.522080
EM: Round [892] log likelihood: -1605.521800
EM: Round [893] log likelihood: -1605.521522
EM: Round [894] log likelihood: -1605.521244
EM: Round [895] log likelihood: -1605.520966
EM: Round [896] log likelihood: -1605.520690
EM: Round [897] log likelihood: -1605.520414
EM: Round [898] log likelihood: -1605.520139
EM: Round [899] log likelihood: -1605.519864
EM: Round [900] log likelihood: -1605.519591
EM: Round [901] log likelihood: -1605.519318
EM: Round [902] log likelihood: -1605.519046
EM: Round [903] log likelihood: -1605.518774
EM: Round [904] log likelihood: -1605.518503
EM: Round [905] log likelihood: -1605.518234
EM: Round [906] log likelihood: -1605.517964
EM: Round [907] log likelihood: -1605.517696
EM: Round [908] log likelihood: -1605.517428
EM: Round [909] log likelihood: -1605.517161
EM: Round [910] log likelihood: -1605.516895
EM: Round [911] log likelihood: -1605.516629
EM: Round [912] log likelihood: -1605.516364
EM: Round [913] log likelihood: -1605.516100
EM: Round [914] log likelihood: -1605.515836
EM: Round [915] log likelihood: -1605.515573
EM: Round [916] log likelihood: -1605.515311
EM: Round [917] log likelihood: -1605.515050
EM: Round [918] log likelihood: -1605.514789
EM: Round [919] log likelihood: -1605.514529
EM: Round [920] log likelihood: -1605.514270
EM: Round [921] log likelihood: -1605.514011
EM: Round [922] log likelihood: -1605.513754
EM: Round [923] log likelihood: -1605.513496
EM: Round [924] log likelihood: -1605.513240
EM: Round [925] log likelihood: -1605.512984
EM: Round [926] log likelihood: -1605.512729
EM: Round [927] log likelihood: -1605.512474
EM: Round [928] log likelihood: -1605.512221
EM: Round [929] log likelihood: -1605.511967
EM: Round [930] log likelihood: -1605.511715
EM: Round [931] log likelihood: -1605.511463
EM: Round [932] log likelihood: -1605.511212
EM: Round [933] log likelihood: -1605.510962
EM: Round [934] log likelihood: -1605.510712
EM: Round [935] log likelihood: -1605.510463
EM: Round [936] log likelihood: -1605.510215
EM: Round [937] log likelihood: -1605.509967
EM: Round [938] log likelihood: -1605.509720
EM: Round [939] log likelihood: -1605.509473
EM: Round [940] log likelihood: -1605.509227
EM: Round [941] log likelihood: -1605.508982
EM: Round [942] log likelihood: -1605.508738
EM: Round [943] log likelihood: -1605.508494
EM: Round [944] log likelihood: -1605.508251
EM: Round [945] log likelihood: -1605.508008
EM: Round [946] log likelihood: -1605.507767
EM: Round [947] log likelihood: -1605.507525
EM: Round [948] log likelihood: -1605.507285
EM: Round [949] log likelihood: -1605.507045
EM: Round [950] log likelihood: -1605.506805
EM: Round [951] log likelihood: -1605.506567
EM: Round [952] log likelihood: -1605.506329
EM: Round [953] log likelihood: -1605.506091
EM: Round [954] log likelihood: -1605.505855
EM: Round [955] log likelihood: -1605.505618
EM: Round [956] log likelihood: -1605.505383
EM: Round [957] log likelihood: -1605.505148
EM: Round [958] log likelihood: -1605.504914
EM: Round [959] log likelihood: -1605.504680
EM: Round [960] log likelihood: -1605.504447
EM: Round [961] log likelihood: -1605.504215
EM: Round [962] log likelihood: -1605.503983
EM: Round [963] log likelihood: -1605.503752
EM: Round [964] log likelihood: -1605.503521
EM: Round [965] log likelihood: -1605.503291
EM: Round [966] log likelihood: -1605.503062
EM: Round [967] log likelihood: -1605.502833
EM: Round [968] log likelihood: -1605.502605
EM: Round [969] log likelihood: -1605.502377
EM: Round [970] log likelihood: -1605.502151
EM: Round [971] log likelihood: -1605.501924
EM: Round [972] log likelihood: -1605.501699
EM: Round [973] log likelihood: -1605.501473
EM: Round [974] log likelihood: -1605.501249
EM: Round [975] log likelihood: -1605.501025
EM: Round [976] log likelihood: -1605.500802
EM: Round [977] log likelihood: -1605.500579
EM: Round [978] log likelihood: -1605.500357
EM: Round [979] log likelihood: -1605.500135
EM: Round [980] log likelihood: -1605.499914
EM: Round [981] log likelihood: -1605.499694
EM: Round [982] log likelihood: -1605.499474
EM: Round [983] log likelihood: -1605.499255
EM: Round [984] log likelihood: -1605.499036
EM: Round [985] log likelihood: -1605.498818
EM: Round [986] log likelihood: -1605.498600
EM: Round [987] log likelihood: -1605.498383
EM: Round [988] log likelihood: -1605.498167
EM: Round [989] log likelihood: -1605.497951
EM: Round [990] log likelihood: -1605.497736
EM: Round [991] log likelihood: -1605.497521
EM: Round [992] log likelihood: -1605.497307
EM: Round [993] log likelihood: -1605.497094
EM: Round [994] log likelihood: -1605.496881
EM: Round [995] log likelihood: -1605.496668
EM: Round [996] log likelihood: -1605.496457
EM: Round [997] log likelihood: -1605.496245
EM: Round [998] log likelihood: -1605.496035
EM: Round [999] log likelihood: -1605.495824
EM: Round [1000] log likelihood: -1605.495615
EM: Round [1001] log likelihood: -1605.495406
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir
-done, see /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -1358.508098
EM: Round [1] log likelihood: -1358.480125
EM: Round [2] log likelihood: -1358.463942
EM: Round [3] log likelihood: -1358.448054
EM: Round [4] log likelihood: -1358.432453
EM: Round [5] log likelihood: -1358.417129
EM: Round [6] log likelihood: -1358.402072
EM: Round [7] log likelihood: -1358.387274
EM: Round [8] log likelihood: -1358.372727
EM: Round [9] log likelihood: -1358.358423
EM: Round [10] log likelihood: -1358.344354
EM: Round [11] log likelihood: -1358.330514
EM: Round [12] log likelihood: -1358.316896
EM: Round [13] log likelihood: -1358.303493
EM: Round [14] log likelihood: -1358.290299
EM: Round [15] log likelihood: -1358.277309
EM: Round [16] log likelihood: -1358.264516
EM: Round [17] log likelihood: -1358.251914
EM: Round [18] log likelihood: -1358.239500
EM: Round [19] log likelihood: -1358.227267
EM: Round [20] log likelihood: -1358.215211
EM: Round [21] log likelihood: -1358.203328
EM: Round [22] log likelihood: -1358.191612
EM: Round [23] log likelihood: -1358.180060
EM: Round [24] log likelihood: -1358.168667
EM: Round [25] log likelihood: -1358.157430
EM: Round [26] log likelihood: -1358.146345
EM: Round [27] log likelihood: -1358.135407
EM: Round [28] log likelihood: -1358.124614
EM: Round [29] log likelihood: -1358.113961
EM: Round [30] log likelihood: -1358.103447
EM: Round [31] log likelihood: -1358.093067
EM: Round [32] log likelihood: -1358.082818
EM: Round [33] log likelihood: -1358.072697
EM: Round [34] log likelihood: -1358.062703
EM: Round [35] log likelihood: -1358.052831
EM: Round [36] log likelihood: -1358.043079
EM: Round [37] log likelihood: -1358.033444
EM: Round [38] log likelihood: -1358.023924
EM: Round [39] log likelihood: -1358.014517
EM: Round [40] log likelihood: -1358.005220
EM: Round [41] log likelihood: -1357.996031
EM: Round [42] log likelihood: -1357.986948
EM: Round [43] log likelihood: -1357.977967
EM: Round [44] log likelihood: -1357.969089
EM: Round [45] log likelihood: -1357.960309
EM: Round [46] log likelihood: -1357.951627
EM: Round [47] log likelihood: -1357.943041
EM: Round [48] log likelihood: -1357.934548
EM: Round [49] log likelihood: -1357.926147
EM: Round [50] log likelihood: -1357.917836
EM: Round [51] log likelihood: -1357.909614
EM: Round [52] log likelihood: -1357.901478
EM: Round [53] log likelihood: -1357.893427
EM: Round [54] log likelihood: -1357.885460
EM: Round [55] log likelihood: -1357.877575
EM: Round [56] log likelihood: -1357.869770
EM: Round [57] log likelihood: -1357.862045
EM: Round [58] log likelihood: -1357.854397
EM: Round [59] log likelihood: -1357.846826
EM: Round [60] log likelihood: -1357.839329
EM: Round [61] log likelihood: -1357.831907
EM: Round [62] log likelihood: -1357.824557
EM: Round [63] log likelihood: -1357.817278
EM: Round [64] log likelihood: -1357.810069
EM: Round [65] log likelihood: -1357.802929
EM: Round [66] log likelihood: -1357.795856
EM: Round [67] log likelihood: -1357.788851
EM: Round [68] log likelihood: -1357.781910
EM: Round [69] log likelihood: -1357.775035
EM: Round [70] log likelihood: -1357.768223
EM: Round [71] log likelihood: -1357.761473
EM: Round [72] log likelihood: -1357.754784
EM: Round [73] log likelihood: -1357.748156
EM: Round [74] log likelihood: -1357.741588
EM: Round [75] log likelihood: -1357.735078
EM: Round [76] log likelihood: -1357.728626
EM: Round [77] log likelihood: -1357.722231
EM: Round [78] log likelihood: -1357.715891
EM: Round [79] log likelihood: -1357.709607
EM: Round [80] log likelihood: -1357.703377
EM: Round [81] log likelihood: -1357.697201
EM: Round [82] log likelihood: -1357.691078
EM: Round [83] log likelihood: -1357.685006
EM: Round [84] log likelihood: -1357.678986
EM: Round [85] log likelihood: -1357.673016
EM: Round [86] log likelihood: -1357.667095
EM: Round [87] log likelihood: -1357.661224
EM: Round [88] log likelihood: -1357.655402
EM: Round [89] log likelihood: -1357.649627
EM: Round [90] log likelihood: -1357.643898
EM: Round [91] log likelihood: -1357.638217
EM: Round [92] log likelihood: -1357.632581
EM: Round [93] log likelihood: -1357.626990
EM: Round [94] log likelihood: -1357.621444
EM: Round [95] log likelihood: -1357.615941
EM: Round [96] log likelihood: -1357.610482
EM: Round [97] log likelihood: -1357.605066
EM: Round [98] log likelihood: -1357.599692
EM: Round [99] log likelihood: -1357.594359
EM: Round [100] log likelihood: -1357.589068
EM: Round [101] log likelihood: -1357.583817
EM: Round [102] log likelihood: -1357.578606
EM: Round [103] log likelihood: -1357.573435
EM: Round [104] log likelihood: -1357.568303
EM: Round [105] log likelihood: -1357.563209
EM: Round [106] log likelihood: -1357.558153
EM: Round [107] log likelihood: -1357.553135
EM: Round [108] log likelihood: -1357.548154
EM: Round [109] log likelihood: -1357.543210
EM: Round [110] log likelihood: -1357.538302
EM: Round [111] log likelihood: -1357.533430
EM: Round [112] log likelihood: -1357.528593
EM: Round [113] log likelihood: -1357.523791
EM: Round [114] log likelihood: -1357.519023
EM: Round [115] log likelihood: -1357.514290
EM: Round [116] log likelihood: -1357.509590
EM: Round [117] log likelihood: -1357.504923
EM: Round [118] log likelihood: -1357.500290
EM: Round [119] log likelihood: -1357.495688
EM: Round [120] log likelihood: -1357.491119
EM: Round [121] log likelihood: -1357.486582
EM: Round [122] log likelihood: -1357.482076
EM: Round [123] log likelihood: -1357.477602
EM: Round [124] log likelihood: -1357.473158
EM: Round [125] log likelihood: -1357.468744
EM: Round [126] log likelihood: -1357.464360
EM: Round [127] log likelihood: -1357.460006
EM: Round [128] log likelihood: -1357.455681
EM: Round [129] log likelihood: -1357.451386
EM: Round [130] log likelihood: -1357.447119
EM: Round [131] log likelihood: -1357.442880
EM: Round [132] log likelihood: -1357.438670
EM: Round [133] log likelihood: -1357.434487
EM: Round [134] log likelihood: -1357.430332
EM: Round [135] log likelihood: -1357.426204
EM: Round [136] log likelihood: -1357.422103
EM: Round [137] log likelihood: -1357.418029
EM: Round [138] log likelihood: -1357.413980
EM: Round [139] log likelihood: -1357.409958
EM: Round [140] log likelihood: -1357.405962
EM: Round [141] log likelihood: -1357.401991
EM: Round [142] log likelihood: -1357.398046
EM: Round [143] log likelihood: -1357.394125
EM: Round [144] log likelihood: -1357.390230
EM: Round [145] log likelihood: -1357.386358
EM: Round [146] log likelihood: -1357.382511
EM: Round [147] log likelihood: -1357.378688
EM: Round [148] log likelihood: -1357.374889
EM: Round [149] log likelihood: -1357.371113
EM: Round [150] log likelihood: -1357.367361
EM: Round [151] log likelihood: -1357.363632
EM: Round [152] log likelihood: -1357.359925
EM: Round [153] log likelihood: -1357.356241
EM: Round [154] log likelihood: -1357.352580
EM: Round [155] log likelihood: -1357.348941
EM: Round [156] log likelihood: -1357.345323
EM: Round [157] log likelihood: -1357.341728
EM: Round [158] log likelihood: -1357.338153
EM: Round [159] log likelihood: -1357.334601
EM: Round [160] log likelihood: -1357.331069
EM: Round [161] log likelihood: -1357.327558
EM: Round [162] log likelihood: -1357.324069
EM: Round [163] log likelihood: -1357.320599
EM: Round [164] log likelihood: -1357.317150
EM: Round [165] log likelihood: -1357.313721
EM: Round [166] log likelihood: -1357.310312
EM: Round [167] log likelihood: -1357.306923
EM: Round [168] log likelihood: -1357.303554
EM: Round [169] log likelihood: -1357.300204
EM: Round [170] log likelihood: -1357.296873
EM: Round [171] log likelihood: -1357.293561
EM: Round [172] log likelihood: -1357.290268
EM: Round [173] log likelihood: -1357.286994
EM: Round [174] log likelihood: -1357.283739
EM: Round [175] log likelihood: -1357.280502
EM: Round [176] log likelihood: -1357.277283
EM: Round [177] log likelihood: -1357.274082
EM: Round [178] log likelihood: -1357.270899
EM: Round [179] log likelihood: -1357.267734
EM: Round [180] log likelihood: -1357.264587
EM: Round [181] log likelihood: -1357.261457
EM: Round [182] log likelihood: -1357.258344
EM: Round [183] log likelihood: -1357.255249
EM: Round [184] log likelihood: -1357.252170
EM: Round [185] log likelihood: -1357.249108
EM: Round [186] log likelihood: -1357.246064
EM: Round [187] log likelihood: -1357.243035
EM: Round [188] log likelihood: -1357.240023
EM: Round [189] log likelihood: -1357.237028
EM: Round [190] log likelihood: -1357.234048
EM: Round [191] log likelihood: -1357.231085
EM: Round [192] log likelihood: -1357.228137
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EM: Round [654] log likelihood: -1356.630985
EM: Round [655] log likelihood: -1356.630458
EM: Round [656] log likelihood: -1356.629933
EM: Round [657] log likelihood: -1356.629409
EM: Round [658] log likelihood: -1356.628886
EM: Round [659] log likelihood: -1356.628365
EM: Round [660] log likelihood: -1356.627846
EM: Round [661] log likelihood: -1356.627328
EM: Round [662] log likelihood: -1356.626812
EM: Round [663] log likelihood: -1356.626297
EM: Round [664] log likelihood: -1356.625783
EM: Round [665] log likelihood: -1356.625272
EM: Round [666] log likelihood: -1356.624761
EM: Round [667] log likelihood: -1356.624252
EM: Round [668] log likelihood: -1356.623745
EM: Round [669] log likelihood: -1356.623239
EM: Round [670] log likelihood: -1356.622735
EM: Round [671] log likelihood: -1356.622232
EM: Round [672] log likelihood: -1356.621731
EM: Round [673] log likelihood: -1356.621231
EM: Round [674] log likelihood: -1356.620732
EM: Round [675] log likelihood: -1356.620235
EM: Round [676] log likelihood: -1356.619740
EM: Round [677] log likelihood: -1356.619245
EM: Round [678] log likelihood: -1356.618753
EM: Round [679] log likelihood: -1356.618261
EM: Round [680] log likelihood: -1356.617772
EM: Round [681] log likelihood: -1356.617283
EM: Round [682] log likelihood: -1356.616796
EM: Round [683] log likelihood: -1356.616311
EM: Round [684] log likelihood: -1356.615826
EM: Round [685] log likelihood: -1356.615344
EM: Round [686] log likelihood: -1356.614862
EM: Round [687] log likelihood: -1356.614382
EM: Round [688] log likelihood: -1356.613904
EM: Round [689] log likelihood: -1356.613427
EM: Round [690] log likelihood: -1356.612951
EM: Round [691] log likelihood: -1356.612476
EM: Round [692] log likelihood: -1356.612003
EM: Round [693] log likelihood: -1356.611532
EM: Round [694] log likelihood: -1356.611061
EM: Round [695] log likelihood: -1356.610592
EM: Round [696] log likelihood: -1356.610125
EM: Round [697] log likelihood: -1356.609658
EM: Round [698] log likelihood: -1356.609194
EM: Round [699] log likelihood: -1356.608730
EM: Round [700] log likelihood: -1356.608268
EM: Round [701] log likelihood: -1356.607807
EM: Round [702] log likelihood: -1356.607347
EM: Round [703] log likelihood: -1356.606889
EM: Round [704] log likelihood: -1356.606432
EM: Round [705] log likelihood: -1356.605976
EM: Round [706] log likelihood: -1356.605522
EM: Round [707] log likelihood: -1356.605069
EM: Round [708] log likelihood: -1356.604617
EM: Round [709] log likelihood: -1356.604167
EM: Round [710] log likelihood: -1356.603718
EM: Round [711] log likelihood: -1356.603270
EM: Round [712] log likelihood: -1356.602823
EM: Round [713] log likelihood: -1356.602378
EM: Round [714] log likelihood: -1356.601934
EM: Round [715] log likelihood: -1356.601492
EM: Round [716] log likelihood: -1356.601050
EM: Round [717] log likelihood: -1356.600610
EM: Round [718] log likelihood: -1356.600171
EM: Round [719] log likelihood: -1356.599733
EM: Round [720] log likelihood: -1356.599297
EM: Round [721] log likelihood: -1356.598862
EM: Round [722] log likelihood: -1356.598428
EM: Round [723] log likelihood: -1356.597995
EM: Round [724] log likelihood: -1356.597564
EM: Round [725] log likelihood: -1356.597133
EM: Round [726] log likelihood: -1356.596704
EM: Round [727] log likelihood: -1356.596277
EM: Round [728] log likelihood: -1356.595850
EM: Round [729] log likelihood: -1356.595425
EM: Round [730] log likelihood: -1356.595001
EM: Round [731] log likelihood: -1356.594578
EM: Round [732] log likelihood: -1356.594156
EM: Round [733] log likelihood: -1356.593735
EM: Round [734] log likelihood: -1356.593316
EM: Round [735] log likelihood: -1356.592898
EM: Round [736] log likelihood: -1356.592481
EM: Round [737] log likelihood: -1356.592065
EM: Round [738] log likelihood: -1356.591650
EM: Round [739] log likelihood: -1356.591237
EM: Round [740] log likelihood: -1356.590825
EM: Round [741] log likelihood: -1356.590414
EM: Round [742] log likelihood: -1356.590004
EM: Round [743] log likelihood: -1356.589595
EM: Round [744] log likelihood: -1356.589187
EM: Round [745] log likelihood: -1356.588781
EM: Round [746] log likelihood: -1356.588376
EM: Round [747] log likelihood: -1356.587971
EM: Round [748] log likelihood: -1356.587568
EM: Round [749] log likelihood: -1356.587167
EM: Round [750] log likelihood: -1356.586766
EM: Round [751] log likelihood: -1356.586366
EM: Round [752] log likelihood: -1356.585968
EM: Round [753] log likelihood: -1356.585570
EM: Round [754] log likelihood: -1356.585174
EM: Round [755] log likelihood: -1356.584779
EM: Round [756] log likelihood: -1356.584385
EM: Round [757] log likelihood: -1356.583992
EM: Round [758] log likelihood: -1356.583600
EM: Round [759] log likelihood: -1356.583210
EM: Round [760] log likelihood: -1356.582820
EM: Round [761] log likelihood: -1356.582431
EM: Round [762] log likelihood: -1356.582044
EM: Round [763] log likelihood: -1356.581658
EM: Round [764] log likelihood: -1356.581272
EM: Round [765] log likelihood: -1356.580888
EM: Round [766] log likelihood: -1356.580505
EM: Round [767] log likelihood: -1356.580123
EM: Round [768] log likelihood: -1356.579742
EM: Round [769] log likelihood: -1356.579362
EM: Round [770] log likelihood: -1356.578983
EM: Round [771] log likelihood: -1356.578606
EM: Round [772] log likelihood: -1356.578229
EM: Round [773] log likelihood: -1356.577853
EM: Round [774] log likelihood: -1356.577479
EM: Round [775] log likelihood: -1356.577105
EM: Round [776] log likelihood: -1356.576733
EM: Round [777] log likelihood: -1356.576361
EM: Round [778] log likelihood: -1356.575991
EM: Round [779] log likelihood: -1356.575621
EM: Round [780] log likelihood: -1356.575253
EM: Round [781] log likelihood: -1356.574886
EM: Round [782] log likelihood: -1356.574519
EM: Round [783] log likelihood: -1356.574154
EM: Round [784] log likelihood: -1356.573790
EM: Round [785] log likelihood: -1356.573427
EM: Round [786] log likelihood: -1356.573064
EM: Round [787] log likelihood: -1356.572703
EM: Round [788] log likelihood: -1356.572343
EM: Round [789] log likelihood: -1356.571984
EM: Round [790] log likelihood: -1356.571625
EM: Round [791] log likelihood: -1356.571268
EM: Round [792] log likelihood: -1356.570912
EM: Round [793] log likelihood: -1356.570557
EM: Round [794] log likelihood: -1356.570202
EM: Round [795] log likelihood: -1356.569849
EM: Round [796] log likelihood: -1356.569497
EM: Round [797] log likelihood: -1356.569145
EM: Round [798] log likelihood: -1356.568795
EM: Round [799] log likelihood: -1356.568446
EM: Round [800] log likelihood: -1356.568097
EM: Round [801] log likelihood: -1356.567750
EM: Round [802] log likelihood: -1356.567403
EM: Round [803] log likelihood: -1356.567058
EM: Round [804] log likelihood: -1356.566713
EM: Round [805] log likelihood: -1356.566369
EM: Round [806] log likelihood: -1356.566027
EM: Round [807] log likelihood: -1356.565685
EM: Round [808] log likelihood: -1356.565344
EM: Round [809] log likelihood: -1356.565004
EM: Round [810] log likelihood: -1356.564665
EM: Round [811] log likelihood: -1356.564327
EM: Round [812] log likelihood: -1356.563990
EM: Round [813] log likelihood: -1356.563654
EM: Round [814] log likelihood: -1356.563319
EM: Round [815] log likelihood: -1356.562985
EM: Round [816] log likelihood: -1356.562651
EM: Round [817] log likelihood: -1356.562319
EM: Round [818] log likelihood: -1356.561988
EM: Round [819] log likelihood: -1356.561657
EM: Round [820] log likelihood: -1356.561327
EM: Round [821] log likelihood: -1356.560998
EM: Round [822] log likelihood: -1356.560671
EM: Round [823] log likelihood: -1356.560344
EM: Round [824] log likelihood: -1356.560018
EM: Round [825] log likelihood: -1356.559692
EM: Round [826] log likelihood: -1356.559368
EM: Round [827] log likelihood: -1356.559045
EM: Round [828] log likelihood: -1356.558722
EM: Round [829] log likelihood: -1356.558400
EM: Round [830] log likelihood: -1356.558080
EM: Round [831] log likelihood: -1356.557760
EM: Round [832] log likelihood: -1356.557441
EM: Round [833] log likelihood: -1356.557123
EM: Round [834] log likelihood: -1356.556805
EM: Round [835] log likelihood: -1356.556489
EM: Round [836] log likelihood: -1356.556174
EM: Round [837] log likelihood: -1356.555859
EM: Round [838] log likelihood: -1356.555545
EM: Round [839] log likelihood: -1356.555232
EM: Round [840] log likelihood: -1356.554920
EM: Round [841] log likelihood: -1356.554609
EM: Round [842] log likelihood: -1356.554298
EM: Round [843] log likelihood: -1356.553989
EM: Round [844] log likelihood: -1356.553680
EM: Round [845] log likelihood: -1356.553372
EM: Round [846] log likelihood: -1356.553065
EM: Round [847] log likelihood: -1356.552759
EM: Round [848] log likelihood: -1356.552454
EM: Round [849] log likelihood: -1356.552149
EM: Round [850] log likelihood: -1356.551846
EM: Round [851] log likelihood: -1356.551543
EM: Round [852] log likelihood: -1356.551241
EM: Round [853] log likelihood: -1356.550940
EM: Round [854] log likelihood: -1356.550639
EM: Round [855] log likelihood: -1356.550340
EM: Round [856] log likelihood: -1356.550041
EM: Round [857] log likelihood: -1356.549743
EM: Round [858] log likelihood: -1356.549446
EM: Round [859] log likelihood: -1356.549150
EM: Round [860] log likelihood: -1356.548854
EM: Round [861] log likelihood: -1356.548559
EM: Round [862] log likelihood: -1356.548266
EM: Round [863] log likelihood: -1356.547972
EM: Round [864] log likelihood: -1356.547680
EM: Round [865] log likelihood: -1356.547389
EM: Round [866] log likelihood: -1356.547098
EM: Round [867] log likelihood: -1356.546808
EM: Round [868] log likelihood: -1356.546519
EM: Round [869] log likelihood: -1356.546230
EM: Round [870] log likelihood: -1356.545943
EM: Round [871] log likelihood: -1356.545656
EM: Round [872] log likelihood: -1356.545370
EM: Round [873] log likelihood: -1356.545085
EM: Round [874] log likelihood: -1356.544800
EM: Round [875] log likelihood: -1356.544516
EM: Round [876] log likelihood: -1356.544233
EM: Round [877] log likelihood: -1356.543951
EM: Round [878] log likelihood: -1356.543670
EM: Round [879] log likelihood: -1356.543389
EM: Round [880] log likelihood: -1356.543109
EM: Round [881] log likelihood: -1356.542830
EM: Round [882] log likelihood: -1356.542552
EM: Round [883] log likelihood: -1356.542274
EM: Round [884] log likelihood: -1356.541997
EM: Round [885] log likelihood: -1356.541721
EM: Round [886] log likelihood: -1356.541446
EM: Round [887] log likelihood: -1356.541171
EM: Round [888] log likelihood: -1356.540897
EM: Round [889] log likelihood: -1356.540624
EM: Round [890] log likelihood: -1356.540351
EM: Round [891] log likelihood: -1356.540080
EM: Round [892] log likelihood: -1356.539809
EM: Round [893] log likelihood: -1356.539538
EM: Round [894] log likelihood: -1356.539269
EM: Round [895] log likelihood: -1356.539000
EM: Round [896] log likelihood: -1356.538732
EM: Round [897] log likelihood: -1356.538465
EM: Round [898] log likelihood: -1356.538198
EM: Round [899] log likelihood: -1356.537932
EM: Round [900] log likelihood: -1356.537667
EM: Round [901] log likelihood: -1356.537402
EM: Round [902] log likelihood: -1356.537139
EM: Round [903] log likelihood: -1356.536876
EM: Round [904] log likelihood: -1356.536613
EM: Round [905] log likelihood: -1356.536351
EM: Round [906] log likelihood: -1356.536090
EM: Round [907] log likelihood: -1356.535830
EM: Round [908] log likelihood: -1356.535571
EM: Round [909] log likelihood: -1356.535312
EM: Round [910] log likelihood: -1356.535054
EM: Round [911] log likelihood: -1356.534796
EM: Round [912] log likelihood: -1356.534539
EM: Round [913] log likelihood: -1356.534283
EM: Round [914] log likelihood: -1356.534028
EM: Round [915] log likelihood: -1356.533773
EM: Round [916] log likelihood: -1356.533519
EM: Round [917] log likelihood: -1356.533266
EM: Round [918] log likelihood: -1356.533013
EM: Round [919] log likelihood: -1356.532761
EM: Round [920] log likelihood: -1356.532509
EM: Round [921] log likelihood: -1356.532259
EM: Round [922] log likelihood: -1356.532009
EM: Round [923] log likelihood: -1356.531759
EM: Round [924] log likelihood: -1356.531511
EM: Round [925] log likelihood: -1356.531263
EM: Round [926] log likelihood: -1356.531015
EM: Round [927] log likelihood: -1356.530769
EM: Round [928] log likelihood: -1356.530523
EM: Round [929] log likelihood: -1356.530277
EM: Round [930] log likelihood: -1356.530032
EM: Round [931] log likelihood: -1356.529788
EM: Round [932] log likelihood: -1356.529545
EM: Round [933] log likelihood: -1356.529302
EM: Round [934] log likelihood: -1356.529060
EM: Round [935] log likelihood: -1356.528819
EM: Round [936] log likelihood: -1356.528578
EM: Round [937] log likelihood: -1356.528338
EM: Round [938] log likelihood: -1356.528098
EM: Round [939] log likelihood: -1356.527859
EM: Round [940] log likelihood: -1356.527621
EM: Round [941] log likelihood: -1356.527383
EM: Round [942] log likelihood: -1356.527146
EM: Round [943] log likelihood: -1356.526910
EM: Round [944] log likelihood: -1356.526674
EM: Round [945] log likelihood: -1356.526439
EM: Round [946] log likelihood: -1356.526204
EM: Round [947] log likelihood: -1356.525970
EM: Round [948] log likelihood: -1356.525737
EM: Round [949] log likelihood: -1356.525504
EM: Round [950] log likelihood: -1356.525272
EM: Round [951] log likelihood: -1356.525041
EM: Round [952] log likelihood: -1356.524810
EM: Round [953] log likelihood: -1356.524580
EM: Round [954] log likelihood: -1356.524350
EM: Round [955] log likelihood: -1356.524121
EM: Round [956] log likelihood: -1356.523893
EM: Round [957] log likelihood: -1356.523665
EM: Round [958] log likelihood: -1356.523438
EM: Round [959] log likelihood: -1356.523211
EM: Round [960] log likelihood: -1356.522985
EM: Round [961] log likelihood: -1356.522760
EM: Round [962] log likelihood: -1356.522535
EM: Round [963] log likelihood: -1356.522311
EM: Round [964] log likelihood: -1356.522088
EM: Round [965] log likelihood: -1356.521865
EM: Round [966] log likelihood: -1356.521642
EM: Round [967] log likelihood: -1356.521420
EM: Round [968] log likelihood: -1356.521199
EM: Round [969] log likelihood: -1356.520979
EM: Round [970] log likelihood: -1356.520758
EM: Round [971] log likelihood: -1356.520539
EM: Round [972] log likelihood: -1356.520320
EM: Round [973] log likelihood: -1356.520102
EM: Round [974] log likelihood: -1356.519884
EM: Round [975] log likelihood: -1356.519667
EM: Round [976] log likelihood: -1356.519450
EM: Round [977] log likelihood: -1356.519234
EM: Round [978] log likelihood: -1356.519019
EM: Round [979] log likelihood: -1356.518804
EM: Round [980] log likelihood: -1356.518590
EM: Round [981] log likelihood: -1356.518376
EM: Round [982] log likelihood: -1356.518163
EM: Round [983] log likelihood: -1356.517950
EM: Round [984] log likelihood: -1356.517738
EM: Round [985] log likelihood: -1356.517526
EM: Round [986] log likelihood: -1356.517315
EM: Round [987] log likelihood: -1356.517105
EM: Round [988] log likelihood: -1356.516895
EM: Round [989] log likelihood: -1356.516686
EM: Round [990] log likelihood: -1356.516477
EM: Round [991] log likelihood: -1356.516269
EM: Round [992] log likelihood: -1356.516061
EM: Round [993] log likelihood: -1356.515854
EM: Round [994] log likelihood: -1356.515648
EM: Round [995] log likelihood: -1356.515442
EM: Round [996] log likelihood: -1356.515236
EM: Round [997] log likelihood: -1356.515031
EM: Round [998] log likelihood: -1356.514827
EM: Round [999] log likelihood: -1356.514623
EM: Round [1000] log likelihood: -1356.514420
EM: Round [1001] log likelihood: -1356.514217
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 295561665
Execution Time = 6.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf  > /tmp/nxf.sA3rneZbym/fi_workdir/microH.dat
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.sA3rneZbym/fi_workdir/microH.dat /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_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.sA3rneZbym/fi_workdir/microH.dat /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.sA3rneZbym --json_outfile /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bNS-T1-TRNA-1_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.sA3rneZbym --json_outfile /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1
Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.00 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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory