Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/30c1d54b764ed0b74fa4125b6a2bfc/tih_rna_sample_00464_B23WHTKLT4_2.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/d2c3c16f7dc188feb68a4b39c74256/.command.sh
  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/b9/d2c3c16f7dc188feb68a4b39c74256/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/5eca28a5dd887b6b587755e0e68529/tih_rna_sample_00464_B23WHTKLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/5eca28a5dd887b6b587755e0e68529/tih_rna_sample_00464_B23WHTKLT4_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 tih_rna_sample_00464_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00464_B23WHTKLT4_2.fusionreport.tsv --gtf /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf > /tmp/nxf.6Gty2GxEcP/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf > /tmp/nxf.6Gty2GxEcP/cytoBand.txt
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed
-parsing GTF file: /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed.sorted.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.bed.sorted.bed.gz
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.bed.tabix.ok
Running: samtools faidx /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00464_B23WHTKLT4_2.star --out_dir /tmp/nxf.6Gty2GxEcP/fi_workdir --reads "/tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 09:19:10 ..... started STAR run
Jun 08 09:19:10 ..... loading genome
Jun 08 09:20:47 ... generating Suffix Array index
Jun 08 09:24:27 ... completed Suffix Array index
Jun 08 09:24:27 ..... processing annotations GTF
Jun 08 09:24:28 ..... inserting junctions into the genome indices
Jun 08 09:25:27 ..... started mapping
Jun 08 09:58:57 ..... finished mapping
Jun 08 09:58:58 ..... started sorting BAM
Jun 08 09:58:59 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00464_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00464_B23WHTKLT4_2.star.sortedByCoord.out.bam
Execution Time = 39.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf --CPU 8 --out_prefix tih_rna_sample_00464_B23WHTKLT4_2.star --out_dir /tmp/nxf.6Gty2GxEcP/fi_workdir --reads "/tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_2.fastp.fastq.gz"
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
09:59:06 : INFO : Done.
Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.sortedByCoord.out.bam   -o /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

[10000]   
[20000]   
[30000]   
[40000]   
[50000]   
[60000]   
[70000]   
[80000]   
[90000]   
[100000]   
[110000]   
[120000]   
[130000]   
[140000]   
[150000]   
[160000]   
[170000]   
[180000]   
[190000]   
[200000]   
[210000]   
[220000]   
[230000]   
[240000]   
[250000]   
[260000]   
[270000]   
[280000]   
[290000]   
[300000]   
[310000]   
[320000]   
[330000]   
[340000]   
[350000]   
[360000]   
[370000]   
[380000]   
[390000]   
[400000]   
[410000]   
[420000]   
[430000]   
[440000]   
[450000]   
[460000]   
[470000]   
[480000]   
[490000]   
[500000]   
[510000]   
[520000]   
[530000]   
[540000]   
[550000]   
[560000]   
[570000]   
[580000]   
[590000]   
[600000]   
[610000]   
[620000]   
[630000]   
[640000]   
[650000]   
[660000]   
[670000]   
[680000]   
[690000]   
[700000]   
[710000]   
[720000]   
[730000]   
[740000]   
[750000]   
[760000]   
[770000]   
[780000]   
[790000]   
[800000]   
[810000]   
[820000]   
[830000]   
[840000]   
[850000]   
[860000]   
[870000]   
[880000]   
[890000]   
[900000]   
[910000]   
[920000]   
[930000]   
[940000]   
[950000]   
[960000]   
[970000]   
[980000]   
[990000]   
[1000000]   
[1010000]   
[1020000]   
[1030000]   
[1040000]   
[1050000]   
[1060000]   
[1070000]   
[1080000]   
[1090000]   
[1100000]   
[1110000]   
[1120000]   
[1130000]   
[1140000]   
[1150000]   
[1160000]   
[1170000]   
[1180000]   
[1190000]   
[1200000]   
[1210000]   -done parsing /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16,
          'low complexity anchor region' => 21,
          'excessive soft clipping' => 8275,
          'small anchor length' => 21,
          'per_id < 96' => 5858,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 19,
          ' ** passed ** ' => 3353,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 272,
          'num genes matched < 2' => 2,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 228,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 16
        };
-writing fusion junction support info.
Execution Time = 0.64 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   -fusion SPANNING read extraction for scaff: AC096582.2--SEPTIN14

[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]   -fusion SPANNING read extraction for scaff: AC244035.1--RHEX

[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]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   
[139000]   
[140000]   
[141000]   
[142000]   
[143000]   
[144000]   
[145000]   
[146000]   
[147000]   
[148000]   
[149000]   
[150000]   
[151000]   
[152000]   
[153000]   
[154000]   
[155000]   
[156000]   
[157000]   
[158000]   
[159000]   
[160000]   
[161000]   
[162000]   
[163000]   
[164000]   
[165000]   
[166000]   
[167000]   
[168000]   
[169000]   
[170000]   
[171000]   
[172000]   
[173000]   
[174000]   
[175000]   
[176000]   
[177000]   
[178000]   
[179000]   
[180000]   
[181000]   
[182000]   
[183000]   
[184000]   
[185000]   
[186000]   
[187000]   
[188000]   
[189000]   
[190000]   
[191000]   
[192000]   
[193000]   
[194000]   
[195000]   
[196000]   
[197000]   
[198000]   
[199000]   
[200000]   
[201000]   
[202000]   
[203000]   
[204000]   
[205000]   
[206000]   
[207000]   
[208000]   
[209000]   
[210000]   
[211000]   
[212000]   
[213000]   
[214000]   
[215000]   
[216000]   
[217000]   
[218000]   
[219000]   
[220000]   
[221000]   
[222000]   
[223000]   
[224000]   
[225000]   
[226000]   
[227000]   
[228000]   
[229000]   
[230000]   
[231000]   
[232000]   
[233000]   
[234000]   
[235000]   
[236000]   
[237000]   
[238000]   
[239000]   
[240000]   
[241000]   
[242000]   
[243000]   
[244000]   
[245000]   
[246000]   
[247000]   
[248000]   
[249000]   
[250000]   
[251000]   
[252000]   
[253000]   
[254000]   
[255000]   
[256000]   
[257000]   
[258000]   
[259000]   
[260000]   
[261000]   
[262000]   
[263000]   
[264000]   
[265000]   
[266000]   
[267000]   
[268000]   
[269000]   
[270000]   
[271000]   
[272000]   
[273000]   
[274000]   
[275000]   
[276000]   
[277000]   
[278000]   
[279000]   
[280000]   
[281000]   
[282000]   
[283000]   
[284000]   
[285000]   
[286000]   
[287000]   
[288000]   
[289000]   
[290000]   
[291000]   
[292000]   
[293000]   
[294000]   
[295000]   
[296000]   
[297000]   
[298000]   
[299000]   
[300000]   
[301000]   
[302000]   
[303000]   
[304000]   
[305000]   
[306000]   
[307000]   
[308000]   
[309000]   
[310000]   
[311000]   
[312000]   
[313000]   
[314000]   
[315000]   
[316000]   
[317000]   
[318000]   
[319000]   
[320000]   
[321000]   
[322000]   
[323000]   
[324000]   
[325000]   
[326000]   
[327000]   
[328000]   
[329000]   
[330000]   
[331000]   
[332000]   
[333000]   
[334000]   
[335000]   
[336000]   
[337000]   
[338000]   
[339000]   
[340000]   
[341000]   
[342000]   
[343000]   
[344000]   
[345000]   
[346000]   
[347000]   
[348000]   
[349000]   
[350000]   
[351000]   
[352000]   
[353000]   
[354000]   
[355000]   
[356000]   
[357000]   
[358000]   
[359000]   
[360000]   
[361000]   
[362000]   
[363000]   
[364000]   
[365000]   
[366000]   
[367000]   
[368000]   
[369000]   
[370000]   
[371000]   
[372000]   
[373000]   
[374000]   
[375000]   
[376000]   
[377000]   
[378000]   
[379000]   
[380000]   
[381000]   
[382000]   
[383000]   
[384000]   
[385000]   
[386000]   
[387000]   
[388000]   
[389000]   
[390000]   
[391000]   
[392000]   
[393000]   
[394000]   
[395000]   
[396000]   
[397000]   
[398000]   
[399000]   
[400000]   
[401000]   
[402000]   
[403000]   
[404000]   
[405000]   
[406000]   
[407000]   
[408000]   
[409000]   
[410000]   
[411000]   
[412000]   
[413000]   
[414000]   
[415000]   
[416000]   
[417000]   
[418000]   
[419000]   
[420000]   
[421000]   
[422000]   
[423000]   
[424000]   
[425000]   
[426000]   
[427000]   
[428000]   
[429000]   
[430000]   
[431000]   
[432000]   
[433000]   
[434000]   
[435000]   
[436000]   
[437000]   
[438000]   
[439000]   
[440000]   
[441000]   
[442000]   
[443000]   
[444000]   
[445000]   
[446000]   
[447000]   
[448000]   
[449000]   
[450000]   
[451000]   
[452000]   
[453000]   
[454000]   
[455000]   
[456000]   
[457000]   
[458000]   
[459000]   
[460000]   
[461000]   
[462000]   
[463000]   
[464000]   
[465000]   
[466000]   
[467000]   
[468000]   
[469000]   
[470000]   
[471000]   
[472000]   
[473000]   
[474000]   
[475000]   
[476000]   
[477000]   
[478000]   
[479000]   
[480000]   
[481000]   
[482000]   
[483000]   
[484000]   
[485000]   
[486000]   
[487000]   
[488000]   
[489000]   
[490000]   
[491000]   
[492000]   
[493000]   
[494000]   
[495000]   
[496000]   
[497000]   
[498000]   
[499000]   
[500000]   
[501000]   
[502000]   
[503000]   
[504000]   
[505000]   
[506000]   
[507000]   
[508000]   
[509000]   
[510000]   
[511000]   
[512000]   
[513000]   
[514000]   
[515000]   
[516000]   
[517000]   
[518000]   
[519000]   
[520000]   
[521000]   
[522000]   
[523000]   
[524000]   
[525000]   
[526000]   
[527000]   
[528000]   
[529000]   
[530000]   
[531000]   
[532000]   
[533000]   
[534000]   
[535000]   
[536000]   
[537000]   
[538000]   
[539000]   
[540000]   
[541000]   
[542000]   
[543000]   
[544000]   
[545000]   
[546000]   
[547000]   
[548000]   
[549000]   
[550000]   
[551000]   
[552000]   
[553000]   
[554000]   
[555000]   
[556000]   
[557000]   
[558000]   
[559000]   
[560000]   
[561000]   
[562000]   
[563000]   
[564000]   
[565000]   
[566000]   
[567000]   
[568000]   
[569000]   
[570000]   
[571000]   
[572000]   
[573000]   
[574000]   
[575000]   
[576000]   
[577000]   
[578000]   
[579000]   
[580000]   
[581000]   
[582000]   
[583000]   
[584000]   
[585000]   
[586000]   
[587000]   
[588000]   
[589000]   
[590000]   
[591000]   
[592000]   
[593000]   
[594000]   
[595000]   
[596000]   
[597000]   
[598000]   
[599000]   
[600000]   
[601000]   
[602000]   
[603000]   
[604000]   
[605000]   
[606000]   
[607000]   
[608000]   
[609000]   
[610000]   
[611000]   
[612000]   
[613000]   
[614000]   
[615000]   
[616000]   
[617000]   
[618000]   
[619000]   
[620000]   
[621000]   
[622000]   
[623000]   
[624000]   
[625000]   
[626000]   
[627000]   
[628000]   
[629000]   
[630000]   
[631000]   
[632000]   
[633000]   
[634000]   
[635000]   
[636000]   
[637000]   
[638000]   
[639000]   
[640000]   
[641000]   
[642000]   
[643000]   
[644000]   
[645000]   
[646000]   
[647000]   
[648000]   
[649000]   
[650000]   
[651000]   
[652000]   
[653000]   
[654000]   
[655000]   
[656000]   
[657000]   
[658000]   
[659000]   
[660000]   
[661000]   
[662000]   
[663000]   
[664000]   
[665000]   
[666000]   
[667000]   
[668000]   
[669000]   
[670000]   -fusion SPANNING read extraction for scaff: ACTBP6--ACTB

[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]   
[121000]   
[122000]   
[123000]   
[124000]   
[125000]   
[126000]   
[127000]   
[128000]   
[129000]   
[130000]   
[131000]   
[132000]   
[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   
[139000]   
[140000]   
[141000]   
[142000]   
[143000]   
[144000]   
[145000]   
[146000]   
[147000]   
[148000]   
[149000]   
[150000]   
[151000]   
[152000]   
[153000]   
[154000]   
[155000]   
[156000]   
[157000]   
[158000]   
[159000]   
[160000]   
[161000]   
[162000]   
[163000]   
[164000]   
[165000]   
[166000]   
[167000]   
[168000]   
[169000]   
[170000]   
[171000]   
[172000]   
[173000]   
[174000]   
[175000]   
[176000]   
[177000]   
[178000]   
[179000]   
[180000]   
[181000]   
[182000]   
[183000]   
[184000]   
[185000]   
[186000]   
[187000]   
[188000]   
[189000]   
[190000]   
[191000]   
[192000]   
[193000]   
[194000]   
[195000]   
[196000]   
[197000]   
[198000]   
[199000]   
[200000]   
[201000]   
[202000]   
[203000]   
[204000]   
[205000]   
[206000]   
[207000]   
[208000]   
[209000]   
[210000]   
[211000]   
[212000]   
[213000]   
[214000]   
[215000]   
[216000]   
[217000]   
[218000]   
[219000]   
[220000]   
[221000]   
[222000]   
[223000]   
[224000]   
[225000]   
[226000]   
[227000]   
[228000]   
[229000]   
[230000]   
[231000]   
[232000]   
[233000]   
[234000]   
[235000]   
[236000]   
[237000]   
[238000]   
[239000]   
[240000]   
[241000]   
[242000]   
[243000]   
[244000]   
[245000]   
[246000]   
[247000]   
[248000]   
[249000]   
[250000]   
[251000]   
[252000]   
[253000]   
[254000]   
[255000]   
[256000]   
[257000]   
[258000]   
[259000]   
[260000]   
[261000]   
[262000]   
[263000]   
[264000]   
[265000]   
[266000]   
[267000]   
[268000]   
[269000]   
[270000]   
[271000]   
[272000]   
[273000]   
[274000]   
[275000]   
[276000]   
[277000]   
[278000]   
[279000]   
[280000]   
[281000]   
[282000]   
[283000]   
[284000]   
[285000]   
[286000]   
[287000]   
[288000]   
[289000]   
[290000]   
[291000]   
[292000]   
[293000]   
[294000]   
[295000]   
[296000]   
[297000]   
[298000]   
[299000]   
[300000]   
[301000]   
[302000]   
[303000]   
[304000]   
[305000]   
[306000]   
[307000]   
[308000]   
[309000]   
[310000]   
[311000]   
[312000]   
[313000]   
[314000]   
[315000]   -fusion SPANNING read extraction for scaff: CANX--CDC25A

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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

[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]   -fusion SPANNING read extraction for scaff: RAB25--PTPRO

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2405
        };
Execution Time = 1.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -3374.394500
EM: Round [1] log likelihood: -3374.025685
EM: Round [2] log likelihood: -3374.022109
EM: Round [3] log likelihood: -3374.019372
EM: Round [4] log likelihood: -3374.016660
EM: Round [5] log likelihood: -3374.013970
EM: Round [6] log likelihood: -3374.011302
EM: Round [7] log likelihood: -3374.008656
EM: Round [8] log likelihood: -3374.006032
EM: Round [9] log likelihood: -3374.003430
EM: Round [10] log likelihood: -3374.000849
EM: Round [11] log likelihood: -3373.998289
EM: Round [12] log likelihood: -3373.995750
EM: Round [13] log likelihood: -3373.993232
EM: Round [14] log likelihood: -3373.990734
EM: Round [15] log likelihood: -3373.988256
EM: Round [16] log likelihood: -3373.985798
EM: Round [17] log likelihood: -3373.983360
EM: Round [18] log likelihood: -3373.980942
EM: Round [19] log likelihood: -3373.978543
EM: Round [20] log likelihood: -3373.976163
EM: Round [21] log likelihood: -3373.973802
EM: Round [22] log likelihood: -3373.971460
EM: Round [23] log likelihood: -3373.969136
EM: Round [24] log likelihood: -3373.966831
EM: Round [25] log likelihood: -3373.964544
EM: Round [26] log likelihood: -3373.962275
EM: Round [27] log likelihood: -3373.960024
EM: Round [28] log likelihood: -3373.957791
EM: Round [29] log likelihood: -3373.955575
EM: Round [30] log likelihood: -3373.953376
EM: Round [31] log likelihood: -3373.951195
EM: Round [32] log likelihood: -3373.949030
EM: Round [33] log likelihood: -3373.946883
EM: Round [34] log likelihood: -3373.944751
EM: Round [35] log likelihood: -3373.942637
EM: Round [36] log likelihood: -3373.940538
EM: Round [37] log likelihood: -3373.938456
EM: Round [38] log likelihood: -3373.936390
EM: Round [39] log likelihood: -3373.934340
EM: Round [40] log likelihood: -3373.932305
EM: Round [41] log likelihood: -3373.930286
EM: Round [42] log likelihood: -3373.928282
EM: Round [43] log likelihood: -3373.926294
EM: Round [44] log likelihood: -3373.924320
EM: Round [45] log likelihood: -3373.922362
EM: Round [46] log likelihood: -3373.920418
EM: Round [47] log likelihood: -3373.918489
EM: Round [48] log likelihood: -3373.916574
EM: Round [49] log likelihood: -3373.914674
EM: Round [50] log likelihood: -3373.912788
EM: Round [51] log likelihood: -3373.910916
EM: Round [52] log likelihood: -3373.909059
EM: Round [53] log likelihood: -3373.907215
EM: Round [54] log likelihood: -3373.905384
EM: Round [55] log likelihood: -3373.903568
EM: Round [56] log likelihood: -3373.901765
EM: Round [57] log likelihood: -3373.899975
EM: Round [58] log likelihood: -3373.898198
EM: Round [59] log likelihood: -3373.896435
EM: Round [60] log likelihood: -3373.894684
EM: Round [61] log likelihood: -3373.892946
EM: Round [62] log likelihood: -3373.891222
EM: Round [63] log likelihood: -3373.889509
EM: Round [64] log likelihood: -3373.887810
EM: Round [65] log likelihood: -3373.886122
EM: Round [66] log likelihood: -3373.884447
EM: Round [67] log likelihood: -3373.882784
EM: Round [68] log likelihood: -3373.881134
EM: Round [69] log likelihood: -3373.879495
EM: Round [70] log likelihood: -3373.877868
EM: Round [71] log likelihood: -3373.876253
EM: Round [72] log likelihood: -3373.874649
EM: Round [73] log likelihood: -3373.873057
EM: Round [74] log likelihood: -3373.871477
EM: Round [75] log likelihood: -3373.869908
EM: Round [76] log likelihood: -3373.868350
EM: Round [77] log likelihood: -3373.866803
EM: Round [78] log likelihood: -3373.865267
EM: Round [79] log likelihood: -3373.863743
EM: Round [80] log likelihood: -3373.862229
EM: Round [81] log likelihood: -3373.860726
EM: Round [82] log likelihood: -3373.859233
EM: Round [83] log likelihood: -3373.857752
EM: Round [84] log likelihood: -3373.856280
EM: Round [85] log likelihood: -3373.854819
EM: Round [86] log likelihood: -3373.853369
EM: Round [87] log likelihood: -3373.851929
EM: Round [88] log likelihood: -3373.850498
EM: Round [89] log likelihood: -3373.849078
EM: Round [90] log likelihood: -3373.847668
EM: Round [91] log likelihood: -3373.846268
EM: Round [92] log likelihood: -3373.844877
EM: Round [93] log likelihood: -3373.843497
EM: Round [94] log likelihood: -3373.842126
EM: Round [95] log likelihood: -3373.840764
EM: Round [96] log likelihood: -3373.839412
EM: Round [97] log likelihood: -3373.838069
EM: Round [98] log likelihood: -3373.836736
EM: Round [99] log likelihood: -3373.835412
EM: Round [100] log likelihood: -3373.834097
EM: Round [101] log likelihood: -3373.832791
EM: Round [102] log likelihood: -3373.831495
EM: Round [103] log likelihood: -3373.830207
EM: Round [104] log likelihood: -3373.828928
EM: Round [105] log likelihood: -3373.827658
EM: Round [106] log likelihood: -3373.826396
EM: Round [107] log likelihood: -3373.825144
EM: Round [108] log likelihood: -3373.823899
EM: Round [109] log likelihood: -3373.822664
EM: Round [110] log likelihood: -3373.821437
EM: Round [111] log likelihood: -3373.820218
EM: Round [112] log likelihood: -3373.819007
EM: Round [113] log likelihood: -3373.817805
EM: Round [114] log likelihood: -3373.816611
EM: Round [115] log likelihood: -3373.815425
EM: Round [116] log likelihood: -3373.814247
EM: Round [117] log likelihood: -3373.813078
EM: Round [118] log likelihood: -3373.811916
EM: Round [119] log likelihood: -3373.810762
EM: Round [120] log likelihood: -3373.809615
EM: Round [121] log likelihood: -3373.808477
EM: Round [122] log likelihood: -3373.807346
EM: Round [123] log likelihood: -3373.806223
EM: Round [124] log likelihood: -3373.805107
EM: Round [125] log likelihood: -3373.803999
EM: Round [126] log likelihood: -3373.802898
EM: Round [127] log likelihood: -3373.801805
EM: Round [128] log likelihood: -3373.800719
EM: Round [129] log likelihood: -3373.799640
EM: Round [130] log likelihood: -3373.798569
EM: Round [131] log likelihood: -3373.797504
EM: Round [132] log likelihood: -3373.796447
EM: Round [133] log likelihood: -3373.795397
EM: Round [134] log likelihood: -3373.794354
EM: Round [135] log likelihood: -3373.793317
EM: Round [136] log likelihood: -3373.792288
EM: Round [137] log likelihood: -3373.791265
EM: Round [138] log likelihood: -3373.790250
EM: Round [139] log likelihood: -3373.789240
EM: Round [140] log likelihood: -3373.788238
EM: Round [141] log likelihood: -3373.787242
EM: Round [142] log likelihood: -3373.786253
EM: Round [143] log likelihood: -3373.785271
EM: Round [144] log likelihood: -3373.784294
EM: Round [145] log likelihood: -3373.783325
EM: Round [146] log likelihood: -3373.782361
EM: Round [147] log likelihood: -3373.781404
EM: Round [148] log likelihood: -3373.780453
EM: Round [149] log likelihood: -3373.779509
EM: Round [150] log likelihood: -3373.778571
EM: Round [151] log likelihood: -3373.777638
EM: Round [152] log likelihood: -3373.776712
EM: Round [153] log likelihood: -3373.775792
EM: Round [154] log likelihood: -3373.774878
EM: Round [155] log likelihood: -3373.773970
EM: Round [156] log likelihood: -3373.773068
EM: Round [157] log likelihood: -3373.772172
EM: Round [158] log likelihood: -3373.771281
EM: Round [159] log likelihood: -3373.770397
EM: Round [160] log likelihood: -3373.769518
EM: Round [161] log likelihood: -3373.768645
EM: Round [162] log likelihood: -3373.767777
EM: Round [163] log likelihood: -3373.766915
EM: Round [164] log likelihood: -3373.766059
EM: Round [165] log likelihood: -3373.765208
EM: Round [166] log likelihood: -3373.764363
EM: Round [167] log likelihood: -3373.763523
EM: Round [168] log likelihood: -3373.762688
EM: Round [169] log likelihood: -3373.761859
EM: Round [170] log likelihood: -3373.761036
EM: Round [171] log likelihood: -3373.760217
EM: Round [172] log likelihood: -3373.759404
EM: Round [173] log likelihood: -3373.758596
EM: Round [174] log likelihood: -3373.757793
EM: Round [175] log likelihood: -3373.756996
EM: Round [176] log likelihood: -3373.756203
EM: Round [177] log likelihood: -3373.755416
EM: Round [178] log likelihood: -3373.754634
EM: Round [179] log likelihood: -3373.753856
EM: Round [180] log likelihood: -3373.753084
EM: Round [181] log likelihood: -3373.752316
EM: Round [182] log likelihood: -3373.751554
EM: Round [183] log likelihood: -3373.750796
EM: Round [184] log likelihood: -3373.750043
EM: Round [185] log likelihood: -3373.749295
EM: Round [186] log likelihood: -3373.748552
EM: Round [187] log likelihood: -3373.747813
EM: Round [188] log likelihood: -3373.747079
EM: Round [189] log likelihood: -3373.746350
EM: Round [190] log likelihood: -3373.745625
EM: Round [191] log likelihood: -3373.744905
EM: Round [192] log likelihood: -3373.744190
EM: Round [193] log likelihood: -3373.743479
EM: Round [194] log likelihood: -3373.742772
EM: Round [195] log likelihood: -3373.742070
EM: Round [196] log likelihood: -3373.741373
EM: Round [197] log likelihood: -3373.740679
EM: Round [198] log likelihood: -3373.739991
EM: Round [199] log likelihood: -3373.739306
EM: Round [200] log likelihood: -3373.738626
EM: Round [201] log likelihood: -3373.737950
EM: Round [202] log likelihood: -3373.737278
EM: Round [203] log likelihood: -3373.736611
EM: Round [204] log likelihood: -3373.735948
EM: Round [205] log likelihood: -3373.735289
EM: Round [206] log likelihood: -3373.734634
EM: Round [207] log likelihood: -3373.733983
EM: Round [208] log likelihood: -3373.733336
EM: Round [209] log likelihood: -3373.732694
EM: Round [210] log likelihood: -3373.732055
EM: Round [211] log likelihood: -3373.731420
EM: Round [212] log likelihood: -3373.730789
EM: Round [213] log likelihood: -3373.730163
EM: Round [214] log likelihood: -3373.729540
EM: Round [215] log likelihood: -3373.728921
EM: Round [216] log likelihood: -3373.728306
EM: Round [217] log likelihood: -3373.727694
EM: Round [218] log likelihood: -3373.727087
EM: Round [219] log likelihood: -3373.726483
EM: Round [220] log likelihood: -3373.725883
EM: Round [221] log likelihood: -3373.725287
EM: Round [222] log likelihood: -3373.724694
EM: Round [223] log likelihood: -3373.724106
EM: Round [224] log likelihood: -3373.723520
EM: Round [225] log likelihood: -3373.722939
EM: Round [226] log likelihood: -3373.722361
EM: Round [227] log likelihood: -3373.721786
EM: Round [228] log likelihood: -3373.721216
EM: Round [229] log likelihood: -3373.720648
EM: Round [230] log likelihood: -3373.720084
EM: Round [231] log likelihood: -3373.719524
EM: Round [232] log likelihood: -3373.718967
EM: Round [233] log likelihood: -3373.718414
EM: Round [234] log likelihood: -3373.717864
EM: Round [235] log likelihood: -3373.717317
EM: Round [236] log likelihood: -3373.716774
EM: Round [237] log likelihood: -3373.716234
EM: Round [238] log likelihood: -3373.715697
EM: Round [239] log likelihood: -3373.715164
EM: Round [240] log likelihood: -3373.714634
EM: Round [241] log likelihood: -3373.714107
EM: Round [242] log likelihood: -3373.713584
EM: Round [243] log likelihood: -3373.713063
EM: Round [244] log likelihood: -3373.712546
EM: Round [245] log likelihood: -3373.712032
EM: Round [246] log likelihood: -3373.711522
EM: Round [247] log likelihood: -3373.711014
EM: Round [248] log likelihood: -3373.710509
EM: Round [249] log likelihood: -3373.710008
EM: Round [250] log likelihood: -3373.709509
EM: Round [251] log likelihood: -3373.709014
EM: Round [252] log likelihood: -3373.708522
EM: Round [253] log likelihood: -3373.708032
EM: Round [254] log likelihood: -3373.707546
EM: Round [255] log likelihood: -3373.707063
EM: Round [256] log likelihood: -3373.706582
EM: Round [257] log likelihood: -3373.706105
EM: Round [258] log likelihood: -3373.705630
EM: Round [259] log likelihood: -3373.705158
EM: Round [260] log likelihood: -3373.704690
EM: Round [261] log likelihood: -3373.704224
EM: Round [262] log likelihood: -3373.703760
EM: Round [263] log likelihood: -3373.703300
EM: Round [264] log likelihood: -3373.702843
EM: Round [265] log likelihood: -3373.702388
EM: Round [266] log likelihood: -3373.701936
EM: Round [267] log likelihood: -3373.701487
EM: Round [268] log likelihood: -3373.701040
EM: Round [269] log likelihood: -3373.700596
EM: Round [270] log likelihood: -3373.700155
EM: Round [271] log likelihood: -3373.699717
EM: Round [272] log likelihood: -3373.699281
EM: Round [273] log likelihood: -3373.698848
EM: Round [274] log likelihood: -3373.698417
EM: Round [275] log likelihood: -3373.697989
EM: Round [276] log likelihood: -3373.697564
EM: Round [277] log likelihood: -3373.697141
EM: Round [278] log likelihood: -3373.696721
EM: Round [279] log likelihood: -3373.696303
EM: Round [280] log likelihood: -3373.695888
EM: Round [281] log likelihood: -3373.695475
EM: Round [282] log likelihood: -3373.695065
EM: Round [283] log likelihood: -3373.694657
EM: Round [284] log likelihood: -3373.694252
EM: Round [285] log likelihood: -3373.693849
EM: Round [286] log likelihood: -3373.693449
EM: Round [287] log likelihood: -3373.693050
EM: Round [288] log likelihood: -3373.692655
EM: Round [289] log likelihood: -3373.692262
EM: Round [290] log likelihood: -3373.691871
EM: Round [291] log likelihood: -3373.691482
EM: Round [292] log likelihood: -3373.691096
EM: Round [293] log likelihood: -3373.690712
EM: Round [294] log likelihood: -3373.690331
EM: Round [295] log likelihood: -3373.689951
EM: Round [296] log likelihood: -3373.689574
EM: Round [297] log likelihood: -3373.689200
EM: Round [298] log likelihood: -3373.688827
EM: Round [299] log likelihood: -3373.688457
EM: Round [300] log likelihood: -3373.688089
EM: Round [301] log likelihood: -3373.687723
EM: Round [302] log likelihood: -3373.687359
EM: Round [303] log likelihood: -3373.686998
EM: Round [304] log likelihood: -3373.686638
EM: Round [305] log likelihood: -3373.686281
EM: Round [306] log likelihood: -3373.685926
EM: Round [307] log likelihood: -3373.685573
EM: Round [308] log likelihood: -3373.685222
EM: Round [309] log likelihood: -3373.684874
EM: Round [310] log likelihood: -3373.684527
EM: Round [311] log likelihood: -3373.684182
EM: Round [312] log likelihood: -3373.683840
EM: Round [313] log likelihood: -3373.683499
EM: Round [314] log likelihood: -3373.683161
EM: Round [315] log likelihood: -3373.682824
EM: Round [316] log likelihood: -3373.682490
EM: Round [317] log likelihood: -3373.682157
EM: Round [318] log likelihood: -3373.681827
EM: Round [319] log likelihood: -3373.681498
EM: Round [320] log likelihood: -3373.681172
EM: Round [321] log likelihood: -3373.680847
EM: Round [322] log likelihood: -3373.680525
EM: Round [323] log likelihood: -3373.680204
EM: Round [324] log likelihood: -3373.679885
EM: Round [325] log likelihood: -3373.679568
EM: Round [326] log likelihood: -3373.679253
EM: Round [327] log likelihood: -3373.678940
EM: Round [328] log likelihood: -3373.678628
EM: Round [329] log likelihood: -3373.678319
EM: Round [330] log likelihood: -3373.678011
EM: Round [331] log likelihood: -3373.677705
EM: Round [332] log likelihood: -3373.677401
EM: Round [333] log likelihood: -3373.677099
EM: Round [334] log likelihood: -3373.676798
EM: Round [335] log likelihood: -3373.676499
EM: Round [336] log likelihood: -3373.676203
EM: Round [337] log likelihood: -3373.675907
EM: Round [338] log likelihood: -3373.675614
EM: Round [339] log likelihood: -3373.675322
EM: Round [340] log likelihood: -3373.675032
EM: Round [341] log likelihood: -3373.674744
EM: Round [342] log likelihood: -3373.674457
EM: Round [343] log likelihood: -3373.674173
EM: Round [344] log likelihood: -3373.673889
EM: Round [345] log likelihood: -3373.673608
EM: Round [346] log likelihood: -3373.673328
EM: Round [347] log likelihood: -3373.673050
EM: Round [348] log likelihood: -3373.672773
EM: Round [349] log likelihood: -3373.672498
EM: Round [350] log likelihood: -3373.672225
EM: Round [351] log likelihood: -3373.671953
EM: Round [352] log likelihood: -3373.671683
EM: Round [353] log likelihood: -3373.671415
EM: Round [354] log likelihood: -3373.671148
EM: Round [355] log likelihood: -3373.670882
EM: Round [356] log likelihood: -3373.670618
EM: Round [357] log likelihood: -3373.670356
EM: Round [358] log likelihood: -3373.670095
EM: Round [359] log likelihood: -3373.669836
EM: Round [360] log likelihood: -3373.669579
EM: Round [361] log likelihood: -3373.669322
EM: Round [362] log likelihood: -3373.669068
EM: Round [363] log likelihood: -3373.668815
EM: Round [364] log likelihood: -3373.668563
EM: Round [365] log likelihood: -3373.668313
EM: Round [366] log likelihood: -3373.668064
EM: Round [367] log likelihood: -3373.667817
EM: Round [368] log likelihood: -3373.667571
EM: Round [369] log likelihood: -3373.667327
EM: Round [370] log likelihood: -3373.667084
EM: Round [371] log likelihood: -3373.666842
EM: Round [372] log likelihood: -3373.666602
EM: Round [373] log likelihood: -3373.666363
EM: Round [374] log likelihood: -3373.666126
EM: Round [375] log likelihood: -3373.665890
EM: Round [376] log likelihood: -3373.665656
EM: Round [377] log likelihood: -3373.665422
EM: Round [378] log likelihood: -3373.665191
EM: Round [379] log likelihood: -3373.664960
EM: Round [380] log likelihood: -3373.664731
EM: Round [381] log likelihood: -3373.664503
EM: Round [382] log likelihood: -3373.664277
EM: Round [383] log likelihood: -3373.664052
EM: Round [384] log likelihood: -3373.663828
EM: Round [385] log likelihood: -3373.663606
EM: Round [386] log likelihood: -3373.663384
EM: Round [387] log likelihood: -3373.663165
EM: Round [388] log likelihood: -3373.662946
EM: Round [389] log likelihood: -3373.662729
EM: Round [390] log likelihood: -3373.662513
EM: Round [391] log likelihood: -3373.662298
EM: Round [392] log likelihood: -3373.662084
EM: Round [393] log likelihood: -3373.661872
EM: Round [394] log likelihood: -3373.661661
EM: Round [395] log likelihood: -3373.661451
EM: Round [396] log likelihood: -3373.661242
EM: Round [397] log likelihood: -3373.661035
EM: Round [398] log likelihood: -3373.660829
EM: Round [399] log likelihood: -3373.660624
EM: Round [400] log likelihood: -3373.660420
EM: Round [401] log likelihood: -3373.660217
EM: Round [402] log likelihood: -3373.660016
EM: Round [403] log likelihood: -3373.659816
EM: Round [404] log likelihood: -3373.659617
EM: Round [405] log likelihood: -3373.659419
EM: Round [406] log likelihood: -3373.659222
EM: Round [407] log likelihood: -3373.659026
EM: Round [408] log likelihood: -3373.658832
EM: Round [409] log likelihood: -3373.658638
EM: Round [410] log likelihood: -3373.658446
EM: Round [411] log likelihood: -3373.658255
EM: Round [412] log likelihood: -3373.658065
EM: Round [413] log likelihood: -3373.657876
EM: Round [414] log likelihood: -3373.657688
EM: Round [415] log likelihood: -3373.657501
EM: Round [416] log likelihood: -3373.657316
EM: Round [417] log likelihood: -3373.657131
EM: Round [418] log likelihood: -3373.656948
EM: Round [419] log likelihood: -3373.656765
EM: Round [420] log likelihood: -3373.656584
EM: Round [421] log likelihood: -3373.656404
EM: Round [422] log likelihood: -3373.656224
EM: Round [423] log likelihood: -3373.656046
EM: Round [424] log likelihood: -3373.655869
EM: Round [425] log likelihood: -3373.655693
EM: Round [426] log likelihood: -3373.655518
EM: Round [427] log likelihood: -3373.655343
EM: Round [428] log likelihood: -3373.655170
EM: Round [429] log likelihood: -3373.654998
EM: Round [430] log likelihood: -3373.654827
EM: Round [431] log likelihood: -3373.654657
EM: Round [432] log likelihood: -3373.654488
EM: Round [433] log likelihood: -3373.654319
EM: Round [434] log likelihood: -3373.654152
EM: Round [435] log likelihood: -3373.653986
EM: Round [436] log likelihood: -3373.653821
EM: Round [437] log likelihood: -3373.653656
EM: Round [438] log likelihood: -3373.653493
EM: Round [439] log likelihood: -3373.653331
EM: Round [440] log likelihood: -3373.653169
EM: Round [441] log likelihood: -3373.653008
EM: Round [442] log likelihood: -3373.652849
EM: Round [443] log likelihood: -3373.652690
EM: Round [444] log likelihood: -3373.652532
EM: Round [445] log likelihood: -3373.652375
EM: Round [446] log likelihood: -3373.652219
EM: Round [447] log likelihood: -3373.652064
EM: Round [448] log likelihood: -3373.651910
EM: Round [449] log likelihood: -3373.651757
EM: Round [450] log likelihood: -3373.651604
EM: Round [451] log likelihood: -3373.651453
EM: Round [452] log likelihood: -3373.651302
EM: Round [453] log likelihood: -3373.651152
EM: Round [454] log likelihood: -3373.651004
EM: Round [455] log likelihood: -3373.650855
EM: Round [456] log likelihood: -3373.650708
EM: Round [457] log likelihood: -3373.650562
EM: Round [458] log likelihood: -3373.650416
EM: Round [459] log likelihood: -3373.650272
EM: Round [460] log likelihood: -3373.650128
EM: Round [461] log likelihood: -3373.649985
EM: Round [462] log likelihood: -3373.649843
EM: Round [463] log likelihood: -3373.649701
EM: Round [464] log likelihood: -3373.649561
EM: Round [465] log likelihood: -3373.649421
EM: Round [466] log likelihood: -3373.649282
EM: Round [467] log likelihood: -3373.649144
EM: Round [468] log likelihood: -3373.649006
EM: Round [469] log likelihood: -3373.648870
EM: Round [470] log likelihood: -3373.648734
EM: Round [471] log likelihood: -3373.648599
EM: Round [472] log likelihood: -3373.648465
EM: Round [473] log likelihood: -3373.648331
EM: Round [474] log likelihood: -3373.648199
EM: Round [475] log likelihood: -3373.648067
EM: Round [476] log likelihood: -3373.647936
EM: Round [477] log likelihood: -3373.647805
EM: Round [478] log likelihood: -3373.647676
EM: Round [479] log likelihood: -3373.647547
EM: Round [480] log likelihood: -3373.647419
EM: Round [481] log likelihood: -3373.647291
EM: Round [482] log likelihood: -3373.647164
EM: Round [483] log likelihood: -3373.647038
EM: Round [484] log likelihood: -3373.646913
EM: Round [485] log likelihood: -3373.646789
EM: Round [486] log likelihood: -3373.646665
EM: Round [487] log likelihood: -3373.646542
EM: Round [488] log likelihood: -3373.646419
EM: Round [489] log likelihood: -3373.646298
EM: Round [490] log likelihood: -3373.646177
EM: Round [491] log likelihood: -3373.646056
EM: Round [492] log likelihood: -3373.645937
EM: Round [493] log likelihood: -3373.645818
EM: Round [494] log likelihood: -3373.645700
EM: Round [495] log likelihood: -3373.645582
EM: Round [496] log likelihood: -3373.645465
EM: Round [497] log likelihood: -3373.645349
EM: Round [498] log likelihood: -3373.645233
EM: Round [499] log likelihood: -3373.645118
EM: Round [500] log likelihood: -3373.645004
EM: Round [501] log likelihood: -3373.644891
EM: Round [502] log likelihood: -3373.644778
EM: Round [503] log likelihood: -3373.644665
EM: Round [504] log likelihood: -3373.644554
EM: Round [505] log likelihood: -3373.644443
EM: Round [506] log likelihood: -3373.644332
EM: Round [507] log likelihood: -3373.644223
EM: Round [508] log likelihood: -3373.644113
EM: Round [509] log likelihood: -3373.644005
EM: Round [510] log likelihood: -3373.643897
EM: Round [511] log likelihood: -3373.643790
EM: Round [512] log likelihood: -3373.643683
EM: Round [513] log likelihood: -3373.643577
EM: Round [514] log likelihood: -3373.643472
EM: Round [515] log likelihood: -3373.643367
EM: Round [516] log likelihood: -3373.643263
EM: Round [517] log likelihood: -3373.643159
EM: Round [518] log likelihood: -3373.643056
EM: Round [519] log likelihood: -3373.642954
EM: Round [520] log likelihood: -3373.642852
EM: Round [521] log likelihood: -3373.642751
EM: Round [522] log likelihood: -3373.642650
EM: Round [523] log likelihood: -3373.642550
EM: Round [524] log likelihood: -3373.642450
EM: Stopping iterations at round 524 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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam"
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa -  | samtools sort -@ 8 - -o /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam || : 
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/tih_rna_sample_00464_B23WHTKLT4_2.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.31 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.FusionJuncSpan
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.Pfam.gff3 
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.Pfam.gff3 > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.Pfam.bed
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.igv.seqsimilar.bed
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa > /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.6Gty2GxEcP/fi_workdir/tih_rna_sample_00464_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir
-done, see /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2161.267330
EM: Round [1] log likelihood: -2161.261790
EM: Round [2] log likelihood: -2161.256311
EM: Round [3] log likelihood: -2161.250893
EM: Round [4] log likelihood: -2161.245535
EM: Round [5] log likelihood: -2161.240234
EM: Round [6] log likelihood: -2161.234992
EM: Round [7] log likelihood: -2161.229805
EM: Round [8] log likelihood: -2161.224675
EM: Round [9] log likelihood: -2161.219599
EM: Round [10] log likelihood: -2161.214577
EM: Round [11] log likelihood: -2161.209609
EM: Round [12] log likelihood: -2161.204692
EM: Round [13] log likelihood: -2161.199827
EM: Round [14] log likelihood: -2161.195013
EM: Round [15] log likelihood: -2161.190249
EM: Round [16] log likelihood: -2161.185533
EM: Round [17] log likelihood: -2161.180867
EM: Round [18] log likelihood: -2161.176248
EM: Round [19] log likelihood: -2161.171676
EM: Round [20] log likelihood: -2161.167150
EM: Round [21] log likelihood: -2161.162670
EM: Round [22] log likelihood: -2161.158235
EM: Round [23] log likelihood: -2161.153844
EM: Round [24] log likelihood: -2161.149497
EM: Round [25] log likelihood: -2161.145193
EM: Round [26] log likelihood: -2161.140931
EM: Round [27] log likelihood: -2161.136712
EM: Round [28] log likelihood: -2161.132533
EM: Round [29] log likelihood: -2161.128396
EM: Round [30] log likelihood: -2161.124298
EM: Round [31] log likelihood: -2161.120240
EM: Round [32] log likelihood: -2161.116222
EM: Round [33] log likelihood: -2161.112241
EM: Round [34] log likelihood: -2161.108299
EM: Round [35] log likelihood: -2161.104394
EM: Round [36] log likelihood: -2161.100527
EM: Round [37] log likelihood: -2161.096695
EM: Round [38] log likelihood: -2161.092900
EM: Round [39] log likelihood: -2161.089140
EM: Round [40] log likelihood: -2161.085416
EM: Round [41] log likelihood: -2161.081726
EM: Round [42] log likelihood: -2161.078070
EM: Round [43] log likelihood: -2161.074448
EM: Round [44] log likelihood: -2161.070859
EM: Round [45] log likelihood: -2161.067303
EM: Round [46] log likelihood: -2161.063780
EM: Round [47] log likelihood: -2161.060288
EM: Round [48] log likelihood: -2161.056829
EM: Round [49] log likelihood: -2161.053400
EM: Round [50] log likelihood: -2161.050003
EM: Round [51] log likelihood: -2161.046636
EM: Round [52] log likelihood: -2161.043299
EM: Round [53] log likelihood: -2161.039992
EM: Round [54] log likelihood: -2161.036714
EM: Round [55] log likelihood: -2161.033465
EM: Round [56] log likelihood: -2161.030245
EM: Round [57] log likelihood: -2161.027053
EM: Round [58] log likelihood: -2161.023890
EM: Round [59] log likelihood: -2161.020754
EM: Round [60] log likelihood: -2161.017645
EM: Round [61] log likelihood: -2161.014563
EM: Round [62] log likelihood: -2161.011508
EM: Round [63] log likelihood: -2161.008480
EM: Round [64] log likelihood: -2161.005477
EM: Round [65] log likelihood: -2161.002500
EM: Round [66] log likelihood: -2160.999549
EM: Round [67] log likelihood: -2160.996623
EM: Round [68] log likelihood: -2160.993722
EM: Round [69] log likelihood: -2160.990845
EM: Round [70] log likelihood: -2160.987993
EM: Round [71] log likelihood: -2160.985165
EM: Round [72] log likelihood: -2160.982361
EM: Round [73] log likelihood: -2160.979580
EM: Round [74] log likelihood: -2160.976822
EM: Round [75] log likelihood: -2160.974088
EM: Round [76] log likelihood: -2160.971376
EM: Round [77] log likelihood: -2160.968687
EM: Round [78] log likelihood: -2160.966020
EM: Round [79] log likelihood: -2160.963375
EM: Round [80] log likelihood: -2160.960752
EM: Round [81] log likelihood: -2160.958150
EM: Round [82] log likelihood: -2160.955570
EM: Round [83] log likelihood: -2160.953010
EM: Round [84] log likelihood: -2160.950472
EM: Round [85] log likelihood: -2160.947954
EM: Round [86] log likelihood: -2160.945457
EM: Round [87] log likelihood: -2160.942980
EM: Round [88] log likelihood: -2160.940522
EM: Round [89] log likelihood: -2160.938085
EM: Round [90] log likelihood: -2160.935667
EM: Round [91] log likelihood: -2160.933269
EM: Round [92] log likelihood: -2160.930889
EM: Round [93] log likelihood: -2160.928529
EM: Round [94] log likelihood: -2160.926187
EM: Round [95] log likelihood: -2160.923864
EM: Round [96] log likelihood: -2160.921560
EM: Round [97] log likelihood: -2160.919273
EM: Round [98] log likelihood: -2160.917005
EM: Round [99] log likelihood: -2160.914755
EM: Round [100] log likelihood: -2160.912522
EM: Round [101] log likelihood: -2160.910306
EM: Round [102] log likelihood: -2160.908108
EM: Round [103] log likelihood: -2160.905927
EM: Round [104] log likelihood: -2160.903763
EM: Round [105] log likelihood: -2160.901616
EM: Round [106] log likelihood: -2160.899485
EM: Round [107] log likelihood: -2160.897371
EM: Round [108] log likelihood: -2160.895273
EM: Round [109] log likelihood: -2160.893192
EM: Round [110] log likelihood: -2160.891126
EM: Round [111] log likelihood: -2160.889076
EM: Round [112] log likelihood: -2160.887042
EM: Round [113] log likelihood: -2160.885023
EM: Round [114] log likelihood: -2160.883020
EM: Round [115] log likelihood: -2160.881032
EM: Round [116] log likelihood: -2160.879059
EM: Round [117] log likelihood: -2160.877101
EM: Round [118] log likelihood: -2160.875157
EM: Round [119] log likelihood: -2160.873229
EM: Round [120] log likelihood: -2160.871315
EM: Round [121] log likelihood: -2160.869415
EM: Round [122] log likelihood: -2160.867529
EM: Round [123] log likelihood: -2160.865658
EM: Round [124] log likelihood: -2160.863801
EM: Round [125] log likelihood: -2160.861957
EM: Round [126] log likelihood: -2160.860127
EM: Round [127] log likelihood: -2160.858311
EM: Round [128] log likelihood: -2160.856508
EM: Round [129] log likelihood: -2160.854719
EM: Round [130] log likelihood: -2160.852943
EM: Round [131] log likelihood: -2160.851179
EM: Round [132] log likelihood: -2160.849429
EM: Round [133] log likelihood: -2160.847692
EM: Round [134] log likelihood: -2160.845968
EM: Round [135] log likelihood: -2160.844256
EM: Round [136] log likelihood: -2160.842556
EM: Round [137] log likelihood: -2160.840869
EM: Round [138] log likelihood: -2160.839195
EM: Round [139] log likelihood: -2160.837532
EM: Round [140] log likelihood: -2160.835882
EM: Round [141] log likelihood: -2160.834244
EM: Round [142] log likelihood: -2160.832617
EM: Round [143] log likelihood: -2160.831002
EM: Round [144] log likelihood: -2160.829399
EM: Round [145] log likelihood: -2160.827807
EM: Round [146] log likelihood: -2160.826227
EM: Round [147] log likelihood: -2160.824658
EM: Round [148] log likelihood: -2160.823101
EM: Round [149] log likelihood: -2160.821555
EM: Round [150] log likelihood: -2160.820019
EM: Round [151] log likelihood: -2160.818495
EM: Round [152] log likelihood: -2160.816981
EM: Round [153] log likelihood: -2160.815479
EM: Round [154] log likelihood: -2160.813986
EM: Round [155] log likelihood: -2160.812505
EM: Round [156] log likelihood: -2160.811034
EM: Round [157] log likelihood: -2160.809573
EM: Round [158] log likelihood: -2160.808123
EM: Round [159] log likelihood: -2160.806683
EM: Round [160] log likelihood: -2160.805253
EM: Round [161] log likelihood: -2160.803833
EM: Round [162] log likelihood: -2160.802424
EM: Round [163] log likelihood: -2160.801024
EM: Round [164] log likelihood: -2160.799633
EM: Round [165] log likelihood: -2160.798253
EM: Round [166] log likelihood: -2160.796882
EM: Round [167] log likelihood: -2160.795521
EM: Round [168] log likelihood: -2160.794169
EM: Round [169] log likelihood: -2160.792827
EM: Round [170] log likelihood: -2160.791494
EM: Round [171] log likelihood: -2160.790170
EM: Round [172] log likelihood: -2160.788855
EM: Round [173] log likelihood: -2160.787550
EM: Round [174] log likelihood: -2160.786253
EM: Round [175] log likelihood: -2160.784966
EM: Round [176] log likelihood: -2160.783687
EM: Round [177] log likelihood: -2160.782417
EM: Round [178] log likelihood: -2160.781156
EM: Round [179] log likelihood: -2160.779904
EM: Round [180] log likelihood: -2160.778660
EM: Round [181] log likelihood: -2160.777425
EM: Round [182] log likelihood: -2160.776198
EM: Round [183] log likelihood: -2160.774979
EM: Round [184] log likelihood: -2160.773769
EM: Round [185] log likelihood: -2160.772567
EM: Round [186] log likelihood: -2160.771373
EM: Round [187] log likelihood: -2160.770187
EM: Round [188] log likelihood: -2160.769010
EM: Round [189] log likelihood: -2160.767840
EM: Round [190] log likelihood: -2160.766679
EM: Round [191] log likelihood: -2160.765525
EM: Round [192] log likelihood: -2160.764379
EM: Round [193] log likelihood: -2160.763240
EM: Round [194] log likelihood: -2160.762110
EM: Round [195] log likelihood: -2160.760987
EM: Round [196] log likelihood: -2160.759871
EM: Round [197] log likelihood: -2160.758763
EM: Round [198] log likelihood: -2160.757663
EM: Round [199] log likelihood: -2160.756570
EM: Round [200] log likelihood: -2160.755484
EM: Round [201] log likelihood: -2160.754406
EM: Round [202] log likelihood: -2160.753334
EM: Round [203] log likelihood: -2160.752270
EM: Round [204] log likelihood: -2160.751213
EM: Round [205] log likelihood: -2160.750163
EM: Round [206] log likelihood: -2160.749120
EM: Round [207] log likelihood: -2160.748084
EM: Round [208] log likelihood: -2160.747055
EM: Round [209] log likelihood: -2160.746032
EM: Round [210] log likelihood: -2160.745017
EM: Round [211] log likelihood: -2160.744008
EM: Round [212] log likelihood: -2160.743006
EM: Round [213] log likelihood: -2160.742010
EM: Round [214] log likelihood: -2160.741021
EM: Round [215] log likelihood: -2160.740039
EM: Round [216] log likelihood: -2160.739063
EM: Round [217] log likelihood: -2160.738093
EM: Round [218] log likelihood: -2160.737130
EM: Round [219] log likelihood: -2160.736173
EM: Round [220] log likelihood: -2160.735223
EM: Round [221] log likelihood: -2160.734278
EM: Round [222] log likelihood: -2160.733340
EM: Round [223] log likelihood: -2160.732408
EM: Round [224] log likelihood: -2160.731482
EM: Round [225] log likelihood: -2160.730562
EM: Round [226] log likelihood: -2160.729649
EM: Round [227] log likelihood: -2160.728741
EM: Round [228] log likelihood: -2160.727839
EM: Round [229] log likelihood: -2160.726943
EM: Round [230] log likelihood: -2160.726052
EM: Round [231] log likelihood: -2160.725168
EM: Round [232] log likelihood: -2160.724289
EM: Round [233] log likelihood: -2160.723416
EM: Round [234] log likelihood: -2160.722549
EM: Round [235] log likelihood: -2160.721687
EM: Round [236] log likelihood: -2160.720831
EM: Round [237] log likelihood: -2160.719980
EM: Round [238] log likelihood: -2160.719135
EM: Round [239] log likelihood: -2160.718295
EM: Round [240] log likelihood: -2160.717461
EM: Round [241] log likelihood: -2160.716632
EM: Round [242] log likelihood: -2160.715809
EM: Round [243] log likelihood: -2160.714990
EM: Round [244] log likelihood: -2160.714177
EM: Round [245] log likelihood: -2160.713370
EM: Round [246] log likelihood: -2160.712567
EM: Round [247] log likelihood: -2160.711770
EM: Round [248] log likelihood: -2160.710977
EM: Round [249] log likelihood: -2160.710190
EM: Round [250] log likelihood: -2160.709408
EM: Round [251] log likelihood: -2160.708631
EM: Round [252] log likelihood: -2160.707858
EM: Round [253] log likelihood: -2160.707091
EM: Round [254] log likelihood: -2160.706329
EM: Round [255] log likelihood: -2160.705571
EM: Round [256] log likelihood: -2160.704818
EM: Round [257] log likelihood: -2160.704070
EM: Round [258] log likelihood: -2160.703327
EM: Round [259] log likelihood: -2160.702589
EM: Round [260] log likelihood: -2160.701855
EM: Round [261] log likelihood: -2160.701126
EM: Round [262] log likelihood: -2160.700401
EM: Round [263] log likelihood: -2160.699681
EM: Round [264] log likelihood: -2160.698966
EM: Round [265] log likelihood: -2160.698255
EM: Round [266] log likelihood: -2160.697549
EM: Round [267] log likelihood: -2160.696847
EM: Round [268] log likelihood: -2160.696149
EM: Round [269] log likelihood: -2160.695456
EM: Round [270] log likelihood: -2160.694768
EM: Round [271] log likelihood: -2160.694083
EM: Round [272] log likelihood: -2160.693403
EM: Round [273] log likelihood: -2160.692728
EM: Round [274] log likelihood: -2160.692056
EM: Round [275] log likelihood: -2160.691389
EM: Round [276] log likelihood: -2160.690726
EM: Round [277] log likelihood: -2160.690067
EM: Round [278] log likelihood: -2160.689412
EM: Round [279] log likelihood: -2160.688761
EM: Round [280] log likelihood: -2160.688115
EM: Round [281] log likelihood: -2160.687472
EM: Round [282] log likelihood: -2160.686833
EM: Round [283] log likelihood: -2160.686199
EM: Round [284] log likelihood: -2160.685568
EM: Round [285] log likelihood: -2160.684942
EM: Round [286] log likelihood: -2160.684319
EM: Round [287] log likelihood: -2160.683700
EM: Round [288] log likelihood: -2160.683085
EM: Round [289] log likelihood: -2160.682474
EM: Round [290] log likelihood: -2160.681866
EM: Round [291] log likelihood: -2160.681263
EM: Round [292] log likelihood: -2160.680663
EM: Round [293] log likelihood: -2160.680067
EM: Round [294] log likelihood: -2160.679474
EM: Round [295] log likelihood: -2160.678886
EM: Round [296] log likelihood: -2160.678301
EM: Round [297] log likelihood: -2160.677719
EM: Round [298] log likelihood: -2160.677141
EM: Round [299] log likelihood: -2160.676567
EM: Round [300] log likelihood: -2160.675996
EM: Round [301] log likelihood: -2160.675429
EM: Round [302] log likelihood: -2160.674865
EM: Round [303] log likelihood: -2160.674305
EM: Round [304] log likelihood: -2160.673748
EM: Round [305] log likelihood: -2160.673195
EM: Round [306] log likelihood: -2160.672645
EM: Round [307] log likelihood: -2160.672099
EM: Round [308] log likelihood: -2160.671555
EM: Round [309] log likelihood: -2160.671016
EM: Round [310] log likelihood: -2160.670479
EM: Round [311] log likelihood: -2160.669946
EM: Round [312] log likelihood: -2160.669416
EM: Round [313] log likelihood: -2160.668889
EM: Round [314] log likelihood: -2160.668366
EM: Round [315] log likelihood: -2160.667846
EM: Round [316] log likelihood: -2160.667329
EM: Round [317] log likelihood: -2160.666815
EM: Round [318] log likelihood: -2160.666304
EM: Round [319] log likelihood: -2160.665796
EM: Round [320] log likelihood: -2160.665292
EM: Round [321] log likelihood: -2160.664791
EM: Round [322] log likelihood: -2160.664292
EM: Round [323] log likelihood: -2160.663797
EM: Round [324] log likelihood: -2160.663305
EM: Round [325] log likelihood: -2160.662816
EM: Round [326] log likelihood: -2160.662329
EM: Round [327] log likelihood: -2160.661846
EM: Round [328] log likelihood: -2160.661366
EM: Round [329] log likelihood: -2160.660888
EM: Round [330] log likelihood: -2160.660414
EM: Round [331] log likelihood: -2160.659942
EM: Round [332] log likelihood: -2160.659473
EM: Round [333] log likelihood: -2160.659007
EM: Round [334] log likelihood: -2160.658544
EM: Round [335] log likelihood: -2160.658084
EM: Round [336] log likelihood: -2160.657627
EM: Round [337] log likelihood: -2160.657172
EM: Round [338] log likelihood: -2160.656720
EM: Round [339] log likelihood: -2160.656271
EM: Round [340] log likelihood: -2160.655824
EM: Round [341] log likelihood: -2160.655381
EM: Round [342] log likelihood: -2160.654940
EM: Round [343] log likelihood: -2160.654501
EM: Round [344] log likelihood: -2160.654065
EM: Round [345] log likelihood: -2160.653632
EM: Round [346] log likelihood: -2160.653202
EM: Round [347] log likelihood: -2160.652774
EM: Round [348] log likelihood: -2160.652349
EM: Round [349] log likelihood: -2160.651926
EM: Round [350] log likelihood: -2160.651506
EM: Round [351] log likelihood: -2160.651088
EM: Round [352] log likelihood: -2160.650673
EM: Round [353] log likelihood: -2160.650260
EM: Round [354] log likelihood: -2160.649850
EM: Round [355] log likelihood: -2160.649443
EM: Round [356] log likelihood: -2160.649037
EM: Round [357] log likelihood: -2160.648635
EM: Round [358] log likelihood: -2160.648234
EM: Round [359] log likelihood: -2160.647836
EM: Round [360] log likelihood: -2160.647441
EM: Round [361] log likelihood: -2160.647048
EM: Round [362] log likelihood: -2160.646657
EM: Round [363] log likelihood: -2160.646268
EM: Round [364] log likelihood: -2160.645882
EM: Round [365] log likelihood: -2160.645498
EM: Round [366] log likelihood: -2160.645117
EM: Round [367] log likelihood: -2160.644738
EM: Round [368] log likelihood: -2160.644361
EM: Round [369] log likelihood: -2160.643986
EM: Round [370] log likelihood: -2160.643614
EM: Round [371] log likelihood: -2160.643243
EM: Round [372] log likelihood: -2160.642875
EM: Round [373] log likelihood: -2160.642510
EM: Round [374] log likelihood: -2160.642146
EM: Round [375] log likelihood: -2160.641785
EM: Round [376] log likelihood: -2160.641425
EM: Round [377] log likelihood: -2160.641068
EM: Round [378] log likelihood: -2160.640713
EM: Round [379] log likelihood: -2160.640360
EM: Round [380] log likelihood: -2160.640010
EM: Round [381] log likelihood: -2160.639661
EM: Round [382] log likelihood: -2160.639314
EM: Round [383] log likelihood: -2160.638970
EM: Round [384] log likelihood: -2160.638627
EM: Round [385] log likelihood: -2160.638287
EM: Round [386] log likelihood: -2160.637948
EM: Round [387] log likelihood: -2160.637612
EM: Round [388] log likelihood: -2160.637278
EM: Round [389] log likelihood: -2160.636945
EM: Round [390] log likelihood: -2160.636615
EM: Round [391] log likelihood: -2160.636286
EM: Round [392] log likelihood: -2160.635960
EM: Round [393] log likelihood: -2160.635635
EM: Round [394] log likelihood: -2160.635313
EM: Round [395] log likelihood: -2160.634992
EM: Round [396] log likelihood: -2160.634673
EM: Round [397] log likelihood: -2160.634356
EM: Round [398] log likelihood: -2160.634041
EM: Round [399] log likelihood: -2160.633728
EM: Round [400] log likelihood: -2160.633417
EM: Round [401] log likelihood: -2160.633107
EM: Round [402] log likelihood: -2160.632799
EM: Round [403] log likelihood: -2160.632494
EM: Round [404] log likelihood: -2160.632190
EM: Round [405] log likelihood: -2160.631887
EM: Round [406] log likelihood: -2160.631587
EM: Round [407] log likelihood: -2160.631288
EM: Round [408] log likelihood: -2160.630991
EM: Round [409] log likelihood: -2160.630696
EM: Round [410] log likelihood: -2160.630403
EM: Round [411] log likelihood: -2160.630111
EM: Round [412] log likelihood: -2160.629821
EM: Round [413] log likelihood: -2160.629533
EM: Round [414] log likelihood: -2160.629247
EM: Round [415] log likelihood: -2160.628962
EM: Round [416] log likelihood: -2160.628679
EM: Round [417] log likelihood: -2160.628397
EM: Round [418] log likelihood: -2160.628117
EM: Round [419] log likelihood: -2160.627839
EM: Round [420] log likelihood: -2160.627563
EM: Round [421] log likelihood: -2160.627288
EM: Round [422] log likelihood: -2160.627015
EM: Round [423] log likelihood: -2160.626743
EM: Round [424] log likelihood: -2160.626473
EM: Round [425] log likelihood: -2160.626204
EM: Round [426] log likelihood: -2160.625937
EM: Round [427] log likelihood: -2160.625672
EM: Round [428] log likelihood: -2160.625408
EM: Round [429] log likelihood: -2160.625146
EM: Round [430] log likelihood: -2160.624885
EM: Round [431] log likelihood: -2160.624626
EM: Round [432] log likelihood: -2160.624369
EM: Round [433] log likelihood: -2160.624113
EM: Round [434] log likelihood: -2160.623858
EM: Round [435] log likelihood: -2160.623605
EM: Round [436] log likelihood: -2160.623353
EM: Round [437] log likelihood: -2160.623103
EM: Round [438] log likelihood: -2160.622854
EM: Round [439] log likelihood: -2160.622607
EM: Round [440] log likelihood: -2160.622361
EM: Round [441] log likelihood: -2160.622117
EM: Round [442] log likelihood: -2160.621874
EM: Round [443] log likelihood: -2160.621633
EM: Round [444] log likelihood: -2160.621393
EM: Round [445] log likelihood: -2160.621154
EM: Round [446] log likelihood: -2160.620917
EM: Round [447] log likelihood: -2160.620681
EM: Round [448] log likelihood: -2160.620446
EM: Round [449] log likelihood: -2160.620213
EM: Round [450] log likelihood: -2160.619982
EM: Round [451] log likelihood: -2160.619751
EM: Round [452] log likelihood: -2160.619522
EM: Round [453] log likelihood: -2160.619294
EM: Round [454] log likelihood: -2160.619068
EM: Round [455] log likelihood: -2160.618843
EM: Round [456] log likelihood: -2160.618619
EM: Round [457] log likelihood: -2160.618397
EM: Round [458] log likelihood: -2160.618176
EM: Round [459] log likelihood: -2160.617956
EM: Round [460] log likelihood: -2160.617737
EM: Round [461] log likelihood: -2160.617520
EM: Round [462] log likelihood: -2160.617304
EM: Round [463] log likelihood: -2160.617089
EM: Round [464] log likelihood: -2160.616876
EM: Round [465] log likelihood: -2160.616663
EM: Round [466] log likelihood: -2160.616452
EM: Round [467] log likelihood: -2160.616242
EM: Round [468] log likelihood: -2160.616034
EM: Round [469] log likelihood: -2160.615827
EM: Round [470] log likelihood: -2160.615620
EM: Round [471] log likelihood: -2160.615415
EM: Round [472] log likelihood: -2160.615212
EM: Round [473] log likelihood: -2160.615009
EM: Round [474] log likelihood: -2160.614808
EM: Round [475] log likelihood: -2160.614607
EM: Round [476] log likelihood: -2160.614408
EM: Round [477] log likelihood: -2160.614211
EM: Round [478] log likelihood: -2160.614014
EM: Round [479] log likelihood: -2160.613818
EM: Round [480] log likelihood: -2160.613624
EM: Round [481] log likelihood: -2160.613430
EM: Round [482] log likelihood: -2160.613238
EM: Round [483] log likelihood: -2160.613047
EM: Round [484] log likelihood: -2160.612857
EM: Round [485] log likelihood: -2160.612668
EM: Round [486] log likelihood: -2160.612480
EM: Round [487] log likelihood: -2160.612294
EM: Round [488] log likelihood: -2160.612108
EM: Round [489] log likelihood: -2160.611924
EM: Round [490] log likelihood: -2160.611740
EM: Round [491] log likelihood: -2160.611558
EM: Round [492] log likelihood: -2160.611376
EM: Round [493] log likelihood: -2160.611196
EM: Round [494] log likelihood: -2160.611017
EM: Round [495] log likelihood: -2160.610839
EM: Round [496] log likelihood: -2160.610661
EM: Round [497] log likelihood: -2160.610485
EM: Round [498] log likelihood: -2160.610310
EM: Round [499] log likelihood: -2160.610136
EM: Round [500] log likelihood: -2160.609963
EM: Round [501] log likelihood: -2160.609791
EM: Round [502] log likelihood: -2160.609620
EM: Round [503] log likelihood: -2160.609449
EM: Round [504] log likelihood: -2160.609280
EM: Round [505] log likelihood: -2160.609112
EM: Round [506] log likelihood: -2160.608945
EM: Round [507] log likelihood: -2160.608779
EM: Round [508] log likelihood: -2160.608614
EM: Round [509] log likelihood: -2160.608449
EM: Round [510] log likelihood: -2160.608286
EM: Round [511] log likelihood: -2160.608123
EM: Round [512] log likelihood: -2160.607962
EM: Round [513] log likelihood: -2160.607801
EM: Round [514] log likelihood: -2160.607642
EM: Round [515] log likelihood: -2160.607483
EM: Round [516] log likelihood: -2160.607325
EM: Round [517] log likelihood: -2160.607169
EM: Round [518] log likelihood: -2160.607013
EM: Round [519] log likelihood: -2160.606857
EM: Round [520] log likelihood: -2160.606703
EM: Round [521] log likelihood: -2160.606550
EM: Round [522] log likelihood: -2160.606398
EM: Round [523] log likelihood: -2160.606246
EM: Round [524] log likelihood: -2160.606096
EM: Round [525] log likelihood: -2160.605946
EM: Round [526] log likelihood: -2160.605797
EM: Round [527] log likelihood: -2160.605649
EM: Round [528] log likelihood: -2160.605502
EM: Round [529] log likelihood: -2160.605355
EM: Round [530] log likelihood: -2160.605210
EM: Round [531] log likelihood: -2160.605065
EM: Round [532] log likelihood: -2160.604921
EM: Round [533] log likelihood: -2160.604778
EM: Round [534] log likelihood: -2160.604636
EM: Round [535] log likelihood: -2160.604495
EM: Round [536] log likelihood: -2160.604354
EM: Round [537] log likelihood: -2160.604215
EM: Round [538] log likelihood: -2160.604076
EM: Round [539] log likelihood: -2160.603937
EM: Round [540] log likelihood: -2160.603800
EM: Round [541] log likelihood: -2160.603664
EM: Round [542] log likelihood: -2160.603528
EM: Round [543] log likelihood: -2160.603393
EM: Round [544] log likelihood: -2160.603259
EM: Round [545] log likelihood: -2160.603125
EM: Round [546] log likelihood: -2160.602993
EM: Round [547] log likelihood: -2160.602861
EM: Round [548] log likelihood: -2160.602730
EM: Round [549] log likelihood: -2160.602599
EM: Round [550] log likelihood: -2160.602470
EM: Round [551] log likelihood: -2160.602341
EM: Round [552] log likelihood: -2160.602212
EM: Round [553] log likelihood: -2160.602085
EM: Round [554] log likelihood: -2160.601958
EM: Round [555] log likelihood: -2160.601832
EM: Round [556] log likelihood: -2160.601707
EM: Round [557] log likelihood: -2160.601583
EM: Round [558] log likelihood: -2160.601459
EM: Round [559] log likelihood: -2160.601336
EM: Round [560] log likelihood: -2160.601213
EM: Round [561] log likelihood: -2160.601092
EM: Round [562] log likelihood: -2160.600971
EM: Round [563] log likelihood: -2160.600850
EM: Round [564] log likelihood: -2160.600731
EM: Round [565] log likelihood: -2160.600612
EM: Round [566] log likelihood: -2160.600494
EM: Round [567] log likelihood: -2160.600376
EM: Round [568] log likelihood: -2160.600259
EM: Round [569] log likelihood: -2160.600143
EM: Round [570] log likelihood: -2160.600028
EM: Round [571] log likelihood: -2160.599913
EM: Round [572] log likelihood: -2160.599798
EM: Round [573] log likelihood: -2160.599685
EM: Round [574] log likelihood: -2160.599572
EM: Round [575] log likelihood: -2160.599460
EM: Round [576] log likelihood: -2160.599348
EM: Round [577] log likelihood: -2160.599237
EM: Round [578] log likelihood: -2160.599127
EM: Round [579] log likelihood: -2160.599017
EM: Round [580] log likelihood: -2160.598908
EM: Round [581] log likelihood: -2160.598800
EM: Round [582] log likelihood: -2160.598692
EM: Round [583] log likelihood: -2160.598584
EM: Round [584] log likelihood: -2160.598478
EM: Round [585] log likelihood: -2160.598372
EM: Round [586] log likelihood: -2160.598266
EM: Round [587] log likelihood: -2160.598162
EM: Round [588] log likelihood: -2160.598057
EM: Round [589] log likelihood: -2160.597954
EM: Round [590] log likelihood: -2160.597851
EM: Round [591] log likelihood: -2160.597748
EM: Round [592] log likelihood: -2160.597647
EM: Round [593] log likelihood: -2160.597545
EM: Round [594] log likelihood: -2160.597445
EM: Round [595] log likelihood: -2160.597345
EM: Round [596] log likelihood: -2160.597245
EM: Stopping iterations at round 596 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.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_1.fastp.fastq.gz: 201478511
Execution Time = 3.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa --gtf /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf  > /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fa --gtf /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.gtf  > /tmp/nxf.6Gty2GxEcP/fi_workdir/microH.dat
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.6Gty2GxEcP/fi_workdir/microH.dat /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.6Gty2GxEcP/fi_workdir/microH.dat /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.6Gty2GxEcP --json_outfile /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00464_B23WHTKLT4_2
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.6Gty2GxEcP --json_outfile /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fusion_inspector_web.json --file_prefix tih_rna_sample_00464_B23WHTKLT4_2
Running: touch /tmp/nxf.6Gty2GxEcP/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.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00464_B23WHTKLT4_2 --html_output /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.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.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00464_B23WHTKLT4_2 --html_output /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.fusion_inspector_web.html
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000226780.1]
WARNING, no entry stored in dbm for [ENSG00000226780.1]
WARNING, no entry stored in dbm for [ENSG00000226780.1]
WARNING, no entry stored in dbm for [ENSG00000226780.1]
WARNING, no entry stored in dbm for [ENSG00000226780.1]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.6Gty2GxEcP/ctat_genome_lib_build_dir > /tmp/nxf.6Gty2GxEcP/tih_rna_sample_00464_B23WHTKLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.6Gty2GxEcP/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory