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/b5/5313ef4ad2752d8c42685ad1008b33/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/5b2777bfb4db992854c0aa79553ba0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/5b2777bfb4db992854c0aa79553ba0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/d168738dce0981bffa4b5abf4afa96/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/d168738dce0981bffa4b5abf4afa96/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/cytoBand.txt
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed
-parsing GTF file: /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.pHsQaijzGO/fi_workdir --reads "/tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:57:50 ..... started STAR run
Jun 08 10:57:50 ..... loading genome
Jun 08 10:59:32 ... generating Suffix Array index
Jun 08 11:03:25 ... completed Suffix Array index
Jun 08 11:03:25 ..... processing annotations GTF
Jun 08 11:03:25 ..... inserting junctions into the genome indices
Jun 08 11:04:28 ..... started mapping
Jun 08 12:07:33 ..... finished mapping
Jun 08 12:07:35 ..... started sorting BAM
Jun 08 12:07:35 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
Execution Time = 69.78 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.pHsQaijzGO/fi_workdir --reads "/tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
12:07:43 : INFO : Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam

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[1310000]   -done parsing /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 6430,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'seq-similar region overlap' => 135,
          'num genes matched < 2' => 22,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2,
          ' ** passed ** ' => 10675,
          'low complexity anchor region' => 2,
          'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
          'exons hit < 2' => 5,
          'small anchor length' => 201,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 69,
          'excessive soft clipping' => 7808,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1
        };
-writing fusion junction support info.
Execution Time = 0.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[42000]   -fusion SPANNING read extraction for scaff: ACCS--DCDC1

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[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
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[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   
[139000]   
[140000]   
[141000]   
[142000]   
[143000]   
[144000]   
[145000]   
[146000]   
[147000]   
[148000]   
[149000]   
[150000]   
[151000]   
[152000]   
[153000]   -fusion SPANNING read extraction for scaff: FRG1--FAT1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: GDAP2--AC133865.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: GDAP2--AC099786.3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[18000]   
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[20000]   
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[26000]   
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[30000]   
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[36000]   
[37000]   
[38000]   
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[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   -fusion SPANNING read extraction for scaff: HK1--CAMK2G

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   -fusion SPANNING read extraction for scaff: INPP5E--SMAD2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PARVA--PRRT1B

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   
[119000]   
[120000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
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[68000]   
[69000]   
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[71000]   
[72000]   
[73000]   
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[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   
[81000]   
[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   
[92000]   
[93000]   
[94000]   
[95000]   
[96000]   
[97000]   
[98000]   
[99000]   
[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   
[113000]   
[114000]   
[115000]   
[116000]   
[117000]   
[118000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[18000]   
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[20000]   
[21000]   
[22000]   
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[37000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[10000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[24000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 28484,
          'lacks exon overlap' => 1995
        };
Execution Time = 1.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4699.296218
EM: Round [1] log likelihood: -4698.723866
EM: Round [2] log likelihood: -4698.202443
EM: Round [3] log likelihood: -4697.723412
EM: Round [4] log likelihood: -4697.281727
EM: Round [5] log likelihood: -4696.873324
EM: Round [6] log likelihood: -4696.494829
EM: Round [7] log likelihood: -4696.143375
EM: Round [8] log likelihood: -4695.816485
EM: Round [9] log likelihood: -4695.511987
EM: Round [10] log likelihood: -4695.227959
EM: Round [11] log likelihood: -4694.962684
EM: Round [12] log likelihood: -4694.714620
EM: Round [13] log likelihood: -4694.482375
EM: Round [14] log likelihood: -4694.264688
EM: Round [15] log likelihood: -4694.060414
EM: Round [16] log likelihood: -4693.868510
EM: Round [17] log likelihood: -4693.688027
EM: Round [18] log likelihood: -4693.518095
EM: Round [19] log likelihood: -4693.357923
EM: Round [20] log likelihood: -4693.206784
EM: Round [21] log likelihood: -4693.064013
EM: Round [22] log likelihood: -4692.929002
EM: Round [23] log likelihood: -4692.801194
EM: Round [24] log likelihood: -4692.680075
EM: Round [25] log likelihood: -4692.565175
EM: Round [26] log likelihood: -4692.456065
EM: Round [27] log likelihood: -4692.352345
EM: Round [28] log likelihood: -4692.253653
EM: Round [29] log likelihood: -4692.159652
EM: Round [30] log likelihood: -4692.070033
EM: Round [31] log likelihood: -4691.984512
EM: Round [32] log likelihood: -4691.902827
EM: Round [33] log likelihood: -4691.824736
EM: Round [34] log likelihood: -4691.750015
EM: Round [35] log likelihood: -4691.678458
EM: Round [36] log likelihood: -4691.609874
EM: Round [37] log likelihood: -4691.544088
EM: Round [38] log likelihood: -4691.480936
EM: Round [39] log likelihood: -4691.420267
EM: Round [40] log likelihood: -4691.361940
EM: Round [41] log likelihood: -4691.305826
EM: Round [42] log likelihood: -4691.251803
EM: Round [43] log likelihood: -4691.199760
EM: Round [44] log likelihood: -4691.149591
EM: Round [45] log likelihood: -4691.101199
EM: Round [46] log likelihood: -4691.054494
EM: Round [47] log likelihood: -4691.009391
EM: Round [48] log likelihood: -4690.965811
EM: Round [49] log likelihood: -4690.923679
EM: Round [50] log likelihood: -4690.882928
EM: Round [51] log likelihood: -4690.843492
EM: Round [52] log likelihood: -4690.805310
EM: Round [53] log likelihood: -4690.768325
EM: Round [54] log likelihood: -4690.732485
EM: Round [55] log likelihood: -4690.697738
EM: Round [56] log likelihood: -4690.664038
EM: Round [57] log likelihood: -4690.631340
EM: Round [58] log likelihood: -4690.599602
EM: Round [59] log likelihood: -4690.568785
EM: Round [60] log likelihood: -4690.538850
EM: Round [61] log likelihood: -4690.509763
EM: Round [62] log likelihood: -4690.481491
EM: Round [63] log likelihood: -4690.454001
EM: Round [64] log likelihood: -4690.427263
EM: Round [65] log likelihood: -4690.401250
EM: Round [66] log likelihood: -4690.375934
EM: Round [67] log likelihood: -4690.351290
EM: Round [68] log likelihood: -4690.327292
EM: Round [69] log likelihood: -4690.303919
EM: Round [70] log likelihood: -4690.281147
EM: Round [71] log likelihood: -4690.258956
EM: Round [72] log likelihood: -4690.237326
EM: Round [73] log likelihood: -4690.216237
EM: Round [74] log likelihood: -4690.195672
EM: Round [75] log likelihood: -4690.175612
EM: Round [76] log likelihood: -4690.156041
EM: Round [77] log likelihood: -4690.136943
EM: Round [78] log likelihood: -4690.118303
EM: Round [79] log likelihood: -4690.100106
EM: Round [80] log likelihood: -4690.082337
EM: Round [81] log likelihood: -4690.064984
EM: Round [82] log likelihood: -4690.048034
EM: Round [83] log likelihood: -4690.031473
EM: Round [84] log likelihood: -4690.015291
EM: Round [85] log likelihood: -4689.999476
EM: Round [86] log likelihood: -4689.984016
EM: Round [87] log likelihood: -4689.968901
EM: Round [88] log likelihood: -4689.954121
EM: Round [89] log likelihood: -4689.939666
EM: Round [90] log likelihood: -4689.925526
EM: Round [91] log likelihood: -4689.911693
EM: Round [92] log likelihood: -4689.898157
EM: Round [93] log likelihood: -4689.884911
EM: Round [94] log likelihood: -4689.871945
EM: Round [95] log likelihood: -4689.859252
EM: Round [96] log likelihood: -4689.846825
EM: Round [97] log likelihood: -4689.834656
EM: Round [98] log likelihood: -4689.822738
EM: Round [99] log likelihood: -4689.811064
EM: Round [100] log likelihood: -4689.799628
EM: Round [101] log likelihood: -4689.788422
EM: Round [102] log likelihood: -4689.777441
EM: Round [103] log likelihood: -4689.766679
EM: Round [104] log likelihood: -4689.756131
EM: Round [105] log likelihood: -4689.745789
EM: Round [106] log likelihood: -4689.735650
EM: Round [107] log likelihood: -4689.725707
EM: Round [108] log likelihood: -4689.715956
EM: Round [109] log likelihood: -4689.706391
EM: Round [110] log likelihood: -4689.697008
EM: Round [111] log likelihood: -4689.687803
EM: Round [112] log likelihood: -4689.678770
EM: Round [113] log likelihood: -4689.669905
EM: Round [114] log likelihood: -4689.661205
EM: Round [115] log likelihood: -4689.652665
EM: Round [116] log likelihood: -4689.644280
EM: Round [117] log likelihood: -4689.636048
EM: Round [118] log likelihood: -4689.627965
EM: Round [119] log likelihood: -4689.620026
EM: Round [120] log likelihood: -4689.612228
EM: Round [121] log likelihood: -4689.604568
EM: Round [122] log likelihood: -4689.597043
EM: Round [123] log likelihood: -4689.589649
EM: Round [124] log likelihood: -4689.582383
EM: Round [125] log likelihood: -4689.575242
EM: Round [126] log likelihood: -4689.568224
EM: Round [127] log likelihood: -4689.561324
EM: Round [128] log likelihood: -4689.554541
EM: Round [129] log likelihood: -4689.547872
EM: Round [130] log likelihood: -4689.541314
EM: Round [131] log likelihood: -4689.534864
EM: Round [132] log likelihood: -4689.528520
EM: Round [133] log likelihood: -4689.522280
EM: Round [134] log likelihood: -4689.516142
EM: Round [135] log likelihood: -4689.510102
EM: Round [136] log likelihood: -4689.504159
EM: Round [137] log likelihood: -4689.498310
EM: Round [138] log likelihood: -4689.492554
EM: Round [139] log likelihood: -4689.486888
EM: Round [140] log likelihood: -4689.481310
EM: Round [141] log likelihood: -4689.475819
EM: Round [142] log likelihood: -4689.470412
EM: Round [143] log likelihood: -4689.465088
EM: Round [144] log likelihood: -4689.459845
EM: Round [145] log likelihood: -4689.454681
EM: Round [146] log likelihood: -4689.449595
EM: Round [147] log likelihood: -4689.444584
EM: Round [148] log likelihood: -4689.439647
EM: Round [149] log likelihood: -4689.434782
EM: Round [150] log likelihood: -4689.429989
EM: Round [151] log likelihood: -4689.425265
EM: Round [152] log likelihood: -4689.420610
EM: Round [153] log likelihood: -4689.416021
EM: Round [154] log likelihood: -4689.411497
EM: Round [155] log likelihood: -4689.407037
EM: Round [156] log likelihood: -4689.402640
EM: Round [157] log likelihood: -4689.398304
EM: Round [158] log likelihood: -4689.394028
EM: Round [159] log likelihood: -4689.389811
EM: Round [160] log likelihood: -4689.385651
EM: Round [161] log likelihood: -4689.381548
EM: Round [162] log likelihood: -4689.377501
EM: Round [163] log likelihood: -4689.373508
EM: Round [164] log likelihood: -4689.369568
EM: Round [165] log likelihood: -4689.365680
EM: Round [166] log likelihood: -4689.361843
EM: Round [167] log likelihood: -4689.358056
EM: Round [168] log likelihood: -4689.354319
EM: Round [169] log likelihood: -4689.350630
EM: Round [170] log likelihood: -4689.346988
EM: Round [171] log likelihood: -4689.343392
EM: Round [172] log likelihood: -4689.339843
EM: Round [173] log likelihood: -4689.336337
EM: Round [174] log likelihood: -4689.332876
EM: Round [175] log likelihood: -4689.329457
EM: Round [176] log likelihood: -4689.326081
EM: Round [177] log likelihood: -4689.322746
EM: Round [178] log likelihood: -4689.319452
EM: Round [179] log likelihood: -4689.316198
EM: Round [180] log likelihood: -4689.312983
EM: Round [181] log likelihood: -4689.309807
EM: Round [182] log likelihood: -4689.306668
EM: Round [183] log likelihood: -4689.303566
EM: Round [184] log likelihood: -4689.300501
EM: Round [185] log likelihood: -4689.297472
EM: Round [186] log likelihood: -4689.294478
EM: Round [187] log likelihood: -4689.291518
EM: Round [188] log likelihood: -4689.288593
EM: Round [189] log likelihood: -4689.285700
EM: Round [190] log likelihood: -4689.282841
EM: Round [191] log likelihood: -4689.280014
EM: Round [192] log likelihood: -4689.277218
EM: Round [193] log likelihood: -4689.274454
EM: Round [194] log likelihood: -4689.271721
EM: Round [195] log likelihood: -4689.269017
EM: Round [196] log likelihood: -4689.266343
EM: Round [197] log likelihood: -4689.263698
EM: Round [198] log likelihood: -4689.261082
EM: Round [199] log likelihood: -4689.258494
EM: Round [200] log likelihood: -4689.255934
EM: Round [201] log likelihood: -4689.253401
EM: Round [202] log likelihood: -4689.250895
EM: Round [203] log likelihood: -4689.248415
EM: Round [204] log likelihood: -4689.245962
EM: Round [205] log likelihood: -4689.243534
EM: Round [206] log likelihood: -4689.241131
EM: Round [207] log likelihood: -4689.238753
EM: Round [208] log likelihood: -4689.236399
EM: Round [209] log likelihood: -4689.234069
EM: Round [210] log likelihood: -4689.231763
EM: Round [211] log likelihood: -4689.229480
EM: Round [212] log likelihood: -4689.227220
EM: Round [213] log likelihood: -4689.224983
EM: Round [214] log likelihood: -4689.222768
EM: Round [215] log likelihood: -4689.220575
EM: Round [216] log likelihood: -4689.218404
EM: Round [217] log likelihood: -4689.216253
EM: Round [218] log likelihood: -4689.214124
EM: Round [219] log likelihood: -4689.212016
EM: Round [220] log likelihood: -4689.209927
EM: Round [221] log likelihood: -4689.207859
EM: Round [222] log likelihood: -4689.205811
EM: Round [223] log likelihood: -4689.203782
EM: Round [224] log likelihood: -4689.201773
EM: Round [225] log likelihood: -4689.199782
EM: Round [226] log likelihood: -4689.197810
EM: Round [227] log likelihood: -4689.195856
EM: Round [228] log likelihood: -4689.193921
EM: Round [229] log likelihood: -4689.192004
EM: Round [230] log likelihood: -4689.190104
EM: Round [231] log likelihood: -4689.188222
EM: Round [232] log likelihood: -4689.186356
EM: Round [233] log likelihood: -4689.184508
EM: Round [234] log likelihood: -4689.182677
EM: Round [235] log likelihood: -4689.180862
EM: Round [236] log likelihood: -4689.179064
EM: Round [237] log likelihood: -4689.177281
EM: Round [238] log likelihood: -4689.175515
EM: Round [239] log likelihood: -4689.173764
EM: Round [240] log likelihood: -4689.172028
EM: Round [241] log likelihood: -4689.170308
EM: Round [242] log likelihood: -4689.168603
EM: Round [243] log likelihood: -4689.166913
EM: Round [244] log likelihood: -4689.165238
EM: Round [245] log likelihood: -4689.163577
EM: Round [246] log likelihood: -4689.161930
EM: Round [247] log likelihood: -4689.160298
EM: Round [248] log likelihood: -4689.158679
EM: Round [249] log likelihood: -4689.157075
EM: Round [250] log likelihood: -4689.155484
EM: Round [251] log likelihood: -4689.153907
EM: Round [252] log likelihood: -4689.152342
EM: Round [253] log likelihood: -4689.150792
EM: Round [254] log likelihood: -4689.149254
EM: Round [255] log likelihood: -4689.147729
EM: Round [256] log likelihood: -4689.146216
EM: Round [257] log likelihood: -4689.144716
EM: Round [258] log likelihood: -4689.143229
EM: Round [259] log likelihood: -4689.141754
EM: Round [260] log likelihood: -4689.140291
EM: Round [261] log likelihood: -4689.138840
EM: Round [262] log likelihood: -4689.137401
EM: Round [263] log likelihood: -4689.135973
EM: Round [264] log likelihood: -4689.134557
EM: Round [265] log likelihood: -4689.133153
EM: Round [266] log likelihood: -4689.131760
EM: Round [267] log likelihood: -4689.130378
EM: Round [268] log likelihood: -4689.129007
EM: Round [269] log likelihood: -4689.127648
EM: Round [270] log likelihood: -4689.126299
EM: Round [271] log likelihood: -4689.124960
EM: Round [272] log likelihood: -4689.123633
EM: Round [273] log likelihood: -4689.122315
EM: Round [274] log likelihood: -4689.121009
EM: Round [275] log likelihood: -4689.119712
EM: Round [276] log likelihood: -4689.118426
EM: Round [277] log likelihood: -4689.117149
EM: Round [278] log likelihood: -4689.115883
EM: Round [279] log likelihood: -4689.114627
EM: Round [280] log likelihood: -4689.113380
EM: Round [281] log likelihood: -4689.112143
EM: Round [282] log likelihood: -4689.110915
EM: Round [283] log likelihood: -4689.109697
EM: Round [284] log likelihood: -4689.108488
EM: Round [285] log likelihood: -4689.107288
EM: Round [286] log likelihood: -4689.106098
EM: Round [287] log likelihood: -4689.104917
EM: Round [288] log likelihood: -4689.103744
EM: Round [289] log likelihood: -4689.102581
EM: Round [290] log likelihood: -4689.101426
EM: Round [291] log likelihood: -4689.100280
EM: Round [292] log likelihood: -4689.099143
EM: Round [293] log likelihood: -4689.098014
EM: Round [294] log likelihood: -4689.096894
EM: Round [295] log likelihood: -4689.095782
EM: Round [296] log likelihood: -4689.094678
EM: Round [297] log likelihood: -4689.093583
EM: Round [298] log likelihood: -4689.092495
EM: Round [299] log likelihood: -4689.091416
EM: Round [300] log likelihood: -4689.090345
EM: Round [301] log likelihood: -4689.089282
EM: Round [302] log likelihood: -4689.088226
EM: Round [303] log likelihood: -4689.087178
EM: Round [304] log likelihood: -4689.086138
EM: Round [305] log likelihood: -4689.085106
EM: Round [306] log likelihood: -4689.084081
EM: Round [307] log likelihood: -4689.083063
EM: Round [308] log likelihood: -4689.082053
EM: Round [309] log likelihood: -4689.081051
EM: Round [310] log likelihood: -4689.080055
EM: Round [311] log likelihood: -4689.079067
EM: Round [312] log likelihood: -4689.078086
EM: Round [313] log likelihood: -4689.077112
EM: Round [314] log likelihood: -4689.076145
EM: Round [315] log likelihood: -4689.075185
EM: Round [316] log likelihood: -4689.074232
EM: Round [317] log likelihood: -4689.073286
EM: Round [318] log likelihood: -4689.072346
EM: Round [319] log likelihood: -4689.071414
EM: Round [320] log likelihood: -4689.070488
EM: Round [321] log likelihood: -4689.069568
EM: Round [322] log likelihood: -4689.068655
EM: Round [323] log likelihood: -4689.067748
EM: Round [324] log likelihood: -4689.066848
EM: Round [325] log likelihood: -4689.065955
EM: Round [326] log likelihood: -4689.065067
EM: Round [327] log likelihood: -4689.064186
EM: Round [328] log likelihood: -4689.063311
EM: Round [329] log likelihood: -4689.062442
EM: Round [330] log likelihood: -4689.061580
EM: Round [331] log likelihood: -4689.060723
EM: Round [332] log likelihood: -4689.059872
EM: Round [333] log likelihood: -4689.059027
EM: Round [334] log likelihood: -4689.058189
EM: Round [335] log likelihood: -4689.057356
EM: Round [336] log likelihood: -4689.056528
EM: Round [337] log likelihood: -4689.055707
EM: Round [338] log likelihood: -4689.054891
EM: Round [339] log likelihood: -4689.054081
EM: Round [340] log likelihood: -4689.053277
EM: Round [341] log likelihood: -4689.052478
EM: Round [342] log likelihood: -4689.051685
EM: Round [343] log likelihood: -4689.050897
EM: Round [344] log likelihood: -4689.050114
EM: Round [345] log likelihood: -4689.049337
EM: Round [346] log likelihood: -4689.048565
EM: Round [347] log likelihood: -4689.047799
EM: Round [348] log likelihood: -4689.047038
EM: Round [349] log likelihood: -4689.046282
EM: Round [350] log likelihood: -4689.045531
EM: Round [351] log likelihood: -4689.044785
EM: Round [352] log likelihood: -4689.044045
EM: Round [353] log likelihood: -4689.043309
EM: Round [354] log likelihood: -4689.042579
EM: Round [355] log likelihood: -4689.041853
EM: Round [356] log likelihood: -4689.041132
EM: Round [357] log likelihood: -4689.040417
EM: Round [358] log likelihood: -4689.039706
EM: Round [359] log likelihood: -4689.039000
EM: Round [360] log likelihood: -4689.038298
EM: Round [361] log likelihood: -4689.037602
EM: Round [362] log likelihood: -4689.036910
EM: Round [363] log likelihood: -4689.036223
EM: Round [364] log likelihood: -4689.035540
EM: Round [365] log likelihood: -4689.034862
EM: Round [366] log likelihood: -4689.034189
EM: Round [367] log likelihood: -4689.033520
EM: Round [368] log likelihood: -4689.032855
EM: Round [369] log likelihood: -4689.032195
EM: Round [370] log likelihood: -4689.031540
EM: Round [371] log likelihood: -4689.030889
EM: Round [372] log likelihood: -4689.030242
EM: Round [373] log likelihood: -4689.029599
EM: Round [374] log likelihood: -4689.028961
EM: Round [375] log likelihood: -4689.028327
EM: Round [376] log likelihood: -4689.027698
EM: Round [377] log likelihood: -4689.027072
EM: Round [378] log likelihood: -4689.026451
EM: Round [379] log likelihood: -4689.025834
EM: Round [380] log likelihood: -4689.025220
EM: Round [381] log likelihood: -4689.024611
EM: Round [382] log likelihood: -4689.024006
EM: Round [383] log likelihood: -4689.023405
EM: Round [384] log likelihood: -4689.022808
EM: Round [385] log likelihood: -4689.022215
EM: Round [386] log likelihood: -4689.021626
EM: Round [387] log likelihood: -4689.021041
EM: Round [388] log likelihood: -4689.020459
EM: Round [389] log likelihood: -4689.019882
EM: Round [390] log likelihood: -4689.019308
EM: Round [391] log likelihood: -4689.018738
EM: Round [392] log likelihood: -4689.018172
EM: Round [393] log likelihood: -4689.017609
EM: Round [394] log likelihood: -4689.017050
EM: Round [395] log likelihood: -4689.016495
EM: Round [396] log likelihood: -4689.015943
EM: Round [397] log likelihood: -4689.015395
EM: Round [398] log likelihood: -4689.014851
EM: Round [399] log likelihood: -4689.014310
EM: Round [400] log likelihood: -4689.013773
EM: Round [401] log likelihood: -4689.013239
EM: Round [402] log likelihood: -4689.012709
EM: Round [403] log likelihood: -4689.012182
EM: Round [404] log likelihood: -4689.011659
EM: Round [405] log likelihood: -4689.011139
EM: Round [406] log likelihood: -4689.010622
EM: Round [407] log likelihood: -4689.010109
EM: Round [408] log likelihood: -4689.009599
EM: Round [409] log likelihood: -4689.009093
EM: Round [410] log likelihood: -4689.008590
EM: Round [411] log likelihood: -4689.008090
EM: Round [412] log likelihood: -4689.007593
EM: Round [413] log likelihood: -4689.007099
EM: Round [414] log likelihood: -4689.006609
EM: Round [415] log likelihood: -4689.006122
EM: Round [416] log likelihood: -4689.005638
EM: Round [417] log likelihood: -4689.005157
EM: Round [418] log likelihood: -4689.004679
EM: Round [419] log likelihood: -4689.004204
EM: Round [420] log likelihood: -4689.003733
EM: Round [421] log likelihood: -4689.003264
EM: Round [422] log likelihood: -4689.002799
EM: Round [423] log likelihood: -4689.002336
EM: Round [424] log likelihood: -4689.001876
EM: Round [425] log likelihood: -4689.001420
EM: Round [426] log likelihood: -4689.000966
EM: Round [427] log likelihood: -4689.000515
EM: Round [428] log likelihood: -4689.000067
EM: Round [429] log likelihood: -4688.999622
EM: Round [430] log likelihood: -4688.999180
EM: Round [431] log likelihood: -4688.998741
EM: Round [432] log likelihood: -4688.998305
EM: Round [433] log likelihood: -4688.997871
EM: Round [434] log likelihood: -4688.997440
EM: Round [435] log likelihood: -4688.997012
EM: Round [436] log likelihood: -4688.996586
EM: Round [437] log likelihood: -4688.996164
EM: Round [438] log likelihood: -4688.995744
EM: Round [439] log likelihood: -4688.995326
EM: Round [440] log likelihood: -4688.994912
EM: Round [441] log likelihood: -4688.994500
EM: Round [442] log likelihood: -4688.994090
EM: Round [443] log likelihood: -4688.993684
EM: Round [444] log likelihood: -4688.993280
EM: Round [445] log likelihood: -4688.992878
EM: Round [446] log likelihood: -4688.992479
EM: Round [447] log likelihood: -4688.992082
EM: Round [448] log likelihood: -4688.991688
EM: Round [449] log likelihood: -4688.991297
EM: Round [450] log likelihood: -4688.990908
EM: Round [451] log likelihood: -4688.990522
EM: Round [452] log likelihood: -4688.990137
EM: Round [453] log likelihood: -4688.989756
EM: Round [454] log likelihood: -4688.989377
EM: Round [455] log likelihood: -4688.989000
EM: Round [456] log likelihood: -4688.988626
EM: Round [457] log likelihood: -4688.988254
EM: Round [458] log likelihood: -4688.987884
EM: Round [459] log likelihood: -4688.987517
EM: Round [460] log likelihood: -4688.987152
EM: Round [461] log likelihood: -4688.986789
EM: Round [462] log likelihood: -4688.986429
EM: Round [463] log likelihood: -4688.986070
EM: Round [464] log likelihood: -4688.985715
EM: Round [465] log likelihood: -4688.985361
EM: Round [466] log likelihood: -4688.985010
EM: Round [467] log likelihood: -4688.984660
EM: Round [468] log likelihood: -4688.984314
EM: Round [469] log likelihood: -4688.983969
EM: Round [470] log likelihood: -4688.983626
EM: Round [471] log likelihood: -4688.983286
EM: Round [472] log likelihood: -4688.982947
EM: Round [473] log likelihood: -4688.982611
EM: Round [474] log likelihood: -4688.982277
EM: Round [475] log likelihood: -4688.981945
EM: Round [476] log likelihood: -4688.981616
EM: Round [477] log likelihood: -4688.981288
EM: Round [478] log likelihood: -4688.980962
EM: Round [479] log likelihood: -4688.980638
EM: Round [480] log likelihood: -4688.980317
EM: Round [481] log likelihood: -4688.979997
EM: Round [482] log likelihood: -4688.979680
EM: Round [483] log likelihood: -4688.979364
EM: Round [484] log likelihood: -4688.979050
EM: Round [485] log likelihood: -4688.978739
EM: Round [486] log likelihood: -4688.978429
EM: Round [487] log likelihood: -4688.978121
EM: Round [488] log likelihood: -4688.977815
EM: Round [489] log likelihood: -4688.977511
EM: Round [490] log likelihood: -4688.977209
EM: Round [491] log likelihood: -4688.976909
EM: Round [492] log likelihood: -4688.976611
EM: Round [493] log likelihood: -4688.976315
EM: Round [494] log likelihood: -4688.976020
EM: Round [495] log likelihood: -4688.975727
EM: Round [496] log likelihood: -4688.975437
EM: Round [497] log likelihood: -4688.975148
EM: Round [498] log likelihood: -4688.974860
EM: Round [499] log likelihood: -4688.974575
EM: Round [500] log likelihood: -4688.974291
EM: Round [501] log likelihood: -4688.974009
EM: Round [502] log likelihood: -4688.973729
EM: Round [503] log likelihood: -4688.973451
EM: Round [504] log likelihood: -4688.973174
EM: Round [505] log likelihood: -4688.972899
EM: Round [506] log likelihood: -4688.972626
EM: Round [507] log likelihood: -4688.972354
EM: Round [508] log likelihood: -4688.972085
EM: Round [509] log likelihood: -4688.971817
EM: Round [510] log likelihood: -4688.971550
EM: Round [511] log likelihood: -4688.971285
EM: Round [512] log likelihood: -4688.971022
EM: Round [513] log likelihood: -4688.970761
EM: Round [514] log likelihood: -4688.970501
EM: Round [515] log likelihood: -4688.970242
EM: Round [516] log likelihood: -4688.969986
EM: Round [517] log likelihood: -4688.969731
EM: Round [518] log likelihood: -4688.969477
EM: Round [519] log likelihood: -4688.969225
EM: Round [520] log likelihood: -4688.968975
EM: Round [521] log likelihood: -4688.968726
EM: Round [522] log likelihood: -4688.968479
EM: Round [523] log likelihood: -4688.968233
EM: Round [524] log likelihood: -4688.967989
EM: Round [525] log likelihood: -4688.967746
EM: Round [526] log likelihood: -4688.967505
EM: Round [527] log likelihood: -4688.967265
EM: Round [528] log likelihood: -4688.967027
EM: Round [529] log likelihood: -4688.966790
EM: Round [530] log likelihood: -4688.966555
EM: Round [531] log likelihood: -4688.966321
EM: Round [532] log likelihood: -4688.966089
EM: Round [533] log likelihood: -4688.965858
EM: Round [534] log likelihood: -4688.965628
EM: Round [535] log likelihood: -4688.965400
EM: Round [536] log likelihood: -4688.965173
EM: Round [537] log likelihood: -4688.964948
EM: Round [538] log likelihood: -4688.964724
EM: Round [539] log likelihood: -4688.964502
EM: Round [540] log likelihood: -4688.964280
EM: Round [541] log likelihood: -4688.964061
EM: Round [542] log likelihood: -4688.963842
EM: Round [543] log likelihood: -4688.963625
EM: Round [544] log likelihood: -4688.963410
EM: Round [545] log likelihood: -4688.963195
EM: Round [546] log likelihood: -4688.962982
EM: Round [547] log likelihood: -4688.962770
EM: Round [548] log likelihood: -4688.962560
EM: Round [549] log likelihood: -4688.962351
EM: Round [550] log likelihood: -4688.962143
EM: Round [551] log likelihood: -4688.961936
EM: Round [552] log likelihood: -4688.961731
EM: Round [553] log likelihood: -4688.961527
EM: Round [554] log likelihood: -4688.961324
EM: Round [555] log likelihood: -4688.961122
EM: Round [556] log likelihood: -4688.960922
EM: Round [557] log likelihood: -4688.960723
EM: Round [558] log likelihood: -4688.960525
EM: Round [559] log likelihood: -4688.960329
EM: Round [560] log likelihood: -4688.960133
EM: Round [561] log likelihood: -4688.959939
EM: Round [562] log likelihood: -4688.959746
EM: Round [563] log likelihood: -4688.959554
EM: Round [564] log likelihood: -4688.959363
EM: Round [565] log likelihood: -4688.959174
EM: Round [566] log likelihood: -4688.958986
EM: Round [567] log likelihood: -4688.958798
EM: Round [568] log likelihood: -4688.958612
EM: Round [569] log likelihood: -4688.958428
EM: Round [570] log likelihood: -4688.958244
EM: Round [571] log likelihood: -4688.958061
EM: Round [572] log likelihood: -4688.957880
EM: Round [573] log likelihood: -4688.957699
EM: Round [574] log likelihood: -4688.957520
EM: Round [575] log likelihood: -4688.957342
EM: Round [576] log likelihood: -4688.957165
EM: Round [577] log likelihood: -4688.956989
EM: Round [578] log likelihood: -4688.956814
EM: Round [579] log likelihood: -4688.956640
EM: Round [580] log likelihood: -4688.956467
EM: Round [581] log likelihood: -4688.956295
EM: Round [582] log likelihood: -4688.956125
EM: Round [583] log likelihood: -4688.955955
EM: Round [584] log likelihood: -4688.955787
EM: Round [585] log likelihood: -4688.955619
EM: Round [586] log likelihood: -4688.955452
EM: Round [587] log likelihood: -4688.955287
EM: Round [588] log likelihood: -4688.955122
EM: Round [589] log likelihood: -4688.954959
EM: Round [590] log likelihood: -4688.954796
EM: Round [591] log likelihood: -4688.954635
EM: Round [592] log likelihood: -4688.954474
EM: Round [593] log likelihood: -4688.954315
EM: Round [594] log likelihood: -4688.954156
EM: Round [595] log likelihood: -4688.953999
EM: Round [596] log likelihood: -4688.953842
EM: Round [597] log likelihood: -4688.953686
EM: Round [598] log likelihood: -4688.953532
EM: Round [599] log likelihood: -4688.953378
EM: Round [600] log likelihood: -4688.953225
EM: Round [601] log likelihood: -4688.953073
EM: Round [602] log likelihood: -4688.952922
EM: Round [603] log likelihood: -4688.952772
EM: Round [604] log likelihood: -4688.952623
EM: Round [605] log likelihood: -4688.952475
EM: Round [606] log likelihood: -4688.952327
EM: Round [607] log likelihood: -4688.952181
EM: Round [608] log likelihood: -4688.952035
EM: Round [609] log likelihood: -4688.951891
EM: Round [610] log likelihood: -4688.951747
EM: Round [611] log likelihood: -4688.951604
EM: Round [612] log likelihood: -4688.951462
EM: Round [613] log likelihood: -4688.951321
EM: Round [614] log likelihood: -4688.951181
EM: Round [615] log likelihood: -4688.951041
EM: Round [616] log likelihood: -4688.950903
EM: Round [617] log likelihood: -4688.950765
EM: Round [618] log likelihood: -4688.950628
EM: Round [619] log likelihood: -4688.950492
EM: Round [620] log likelihood: -4688.950357
EM: Round [621] log likelihood: -4688.950222
EM: Round [622] log likelihood: -4688.950089
EM: Round [623] log likelihood: -4688.949956
EM: Round [624] log likelihood: -4688.949824
EM: Round [625] log likelihood: -4688.949693
EM: Round [626] log likelihood: -4688.949562
EM: Round [627] log likelihood: -4688.949433
EM: Round [628] log likelihood: -4688.949304
EM: Round [629] log likelihood: -4688.949176
EM: Round [630] log likelihood: -4688.949049
EM: Round [631] log likelihood: -4688.948922
EM: Round [632] log likelihood: -4688.948796
EM: Round [633] log likelihood: -4688.948671
EM: Round [634] log likelihood: -4688.948547
EM: Round [635] log likelihood: -4688.948424
EM: Round [636] log likelihood: -4688.948301
EM: Round [637] log likelihood: -4688.948179
EM: Round [638] log likelihood: -4688.948058
EM: Round [639] log likelihood: -4688.947938
EM: Round [640] log likelihood: -4688.947818
EM: Round [641] log likelihood: -4688.947699
EM: Round [642] log likelihood: -4688.947581
EM: Round [643] log likelihood: -4688.947463
EM: Round [644] log likelihood: -4688.947346
EM: Round [645] log likelihood: -4688.947230
EM: Round [646] log likelihood: -4688.947115
EM: Round [647] log likelihood: -4688.947000
EM: Round [648] log likelihood: -4688.946886
EM: Round [649] log likelihood: -4688.946773
EM: Round [650] log likelihood: -4688.946660
EM: Round [651] log likelihood: -4688.946548
EM: Round [652] log likelihood: -4688.946437
EM: Round [653] log likelihood: -4688.946326
EM: Round [654] log likelihood: -4688.946216
EM: Round [655] log likelihood: -4688.946107
EM: Round [656] log likelihood: -4688.945998
EM: Round [657] log likelihood: -4688.945890
EM: Round [658] log likelihood: -4688.945783
EM: Round [659] log likelihood: -4688.945676
EM: Round [660] log likelihood: -4688.945570
EM: Round [661] log likelihood: -4688.945465
EM: Round [662] log likelihood: -4688.945360
EM: Round [663] log likelihood: -4688.945256
EM: Round [664] log likelihood: -4688.945153
EM: Round [665] log likelihood: -4688.945050
EM: Round [666] log likelihood: -4688.944948
EM: Round [667] log likelihood: -4688.944846
EM: Round [668] log likelihood: -4688.944745
EM: Round [669] log likelihood: -4688.944645
EM: Round [670] log likelihood: -4688.944545
EM: Stopping iterations at round 670 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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : 
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir
-done, see /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4126.677716
EM: Round [1] log likelihood: -4126.675592
EM: Round [2] log likelihood: -4126.675576
EM: Stopping iterations at round 2 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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 294060824
Execution Time = 5.57 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  > /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  > /tmp/nxf.pHsQaijzGO/fi_workdir/microH.dat
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.pHsQaijzGO/fi_workdir/microH.dat /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.pHsQaijzGO/fi_workdir/microH.dat /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.pHsQaijzGO --json_outfile /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.pHsQaijzGO --json_outfile /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2
Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory