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/68/098d0d7fe3b648f937e15b429fb639/tih_rna_sample_00701_B23MVV7LT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/b9058e06b8af90a932515c2a3b1bcf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/c8117d8e278393332a7a5311a4a763/tih_rna_sample_00701_B23MVV7LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/b9058e06b8af90a932515c2a3b1bcf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/c8117d8e278393332a7a5311a4a763/tih_rna_sample_00701_B23MVV7LT4_1_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_00701_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00701_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf > /tmp/nxf.49np787MMv/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf > /tmp/nxf.49np787MMv/cytoBand.txt
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed
-parsing GTF file: /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00701_B23MVV7LT4_1.star --out_dir /tmp/nxf.49np787MMv/fi_workdir --reads "/tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.49np787MMv/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.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:10:33 ..... started STAR run
Jun 08 10:10:33 ..... loading genome
Jun 08 10:12:17 ... generating Suffix Array index
Jun 08 10:16:12 ... completed Suffix Array index
Jun 08 10:16:12 ..... processing annotations GTF
Jun 08 10:16:13 ..... inserting junctions into the genome indices
Jun 08 10:17:14 ..... started mapping
Jun 08 11:17:10 ..... finished mapping
Jun 08 11:17:12 ..... started sorting BAM
Jun 08 11:17:13 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00701_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00701_B23MVV7LT4_1.star.sortedByCoord.out.bam
Execution Time = 66.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00701_B23MVV7LT4_1.star --out_dir /tmp/nxf.49np787MMv/fi_workdir --reads "/tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:17:20 : INFO : Done.
Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.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]   -done parsing /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          'num genes matched < 2' => 55,
          ' ** passed ** ' => 4121,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 138,
          'per_id < 96' => 2647,
          'excessive soft clipping' => 7935,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 163,
          'seq-similar region overlap' => 57,
          'small anchor length' => 23,
          'low complexity anchor region' => 7,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 14,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 18,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 21
        };
-writing fusion junction support info.
Execution Time = 0.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: AC006008.1--ACTR3B

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: AC092666.1--ACTR3B

[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]   -fusion SPANNING read extraction for scaff: AC136431.1--PKD1P5

[1000]   -fusion SPANNING read extraction for scaff: AC242842.2--BX284613.2

[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: ADK--ASCC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

[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]   -fusion SPANNING read extraction for scaff: FAM83F--TCF20

[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]   -fusion SPANNING read extraction for scaff: FGD4--AL050309.1

[1000]   -fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2

[1000]   -fusion SPANNING read extraction for scaff: LINC00381--NKAIN2

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: LINC00623--BX284613.2

[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]   -fusion SPANNING read extraction for scaff: NOTCH1--INPP5E

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -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]   -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]   
[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]   -fusion SPANNING read extraction for scaff: RPS24--ATP2B2

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

[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]   -fusion SPANNING read extraction for scaff: TFCP2--DAOA-AS1

[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]   -fusion SPANNING read extraction for scaff: TFCP2--AL359745.1

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[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]   -fusion SPANNING read extraction for scaff: TRIM13--TNFSF13B

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: ZNF131--CDH18
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 13930,
          'lacks exon overlap' => 5299
        };
Execution Time = 1.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -6425.874696
EM: Round [1] log likelihood: -6409.331357
EM: Round [2] log likelihood: -6406.563004
EM: Round [3] log likelihood: -6405.543484
EM: Round [4] log likelihood: -6404.827583
EM: Round [5] log likelihood: -6404.253193
EM: Round [6] log likelihood: -6403.783147
EM: Round [7] log likelihood: -6403.395392
EM: Round [8] log likelihood: -6403.073643
EM: Round [9] log likelihood: -6402.805377
EM: Round [10] log likelihood: -6402.580774
EM: Round [11] log likelihood: -6402.392024
EM: Round [12] log likelihood: -6402.232851
EM: Round [13] log likelihood: -6402.098168
EM: Round [14] log likelihood: -6401.983826
EM: Round [15] log likelihood: -6401.886426
EM: Round [16] log likelihood: -6401.803169
EM: Round [17] log likelihood: -6401.731744
EM: Round [18] log likelihood: -6401.670236
EM: Round [19] log likelihood: -6401.617059
EM: Round [20] log likelihood: -6401.570891
EM: Round [21] log likelihood: -6401.530632
EM: Round [22] log likelihood: -6401.495364
EM: Round [23] log likelihood: -6401.464320
EM: Round [24] log likelihood: -6401.436859
EM: Round [25] log likelihood: -6401.412443
EM: Round [26] log likelihood: -6401.390621
EM: Round [27] log likelihood: -6401.371016
EM: Round [28] log likelihood: -6401.353309
EM: Round [29] log likelihood: -6401.337233
EM: Round [30] log likelihood: -6401.322562
EM: Round [31] log likelihood: -6401.309106
EM: Round [32] log likelihood: -6401.296704
EM: Round [33] log likelihood: -6401.285222
EM: Round [34] log likelihood: -6401.274542
EM: Round [35] log likelihood: -6401.264568
EM: Round [36] log likelihood: -6401.255216
EM: Round [37] log likelihood: -6401.246415
EM: Round [38] log likelihood: -6401.238105
EM: Round [39] log likelihood: -6401.230234
EM: Round [40] log likelihood: -6401.222757
EM: Round [41] log likelihood: -6401.215636
EM: Round [42] log likelihood: -6401.208837
EM: Round [43] log likelihood: -6401.202332
EM: Round [44] log likelihood: -6401.196096
EM: Round [45] log likelihood: -6401.190107
EM: Round [46] log likelihood: -6401.184346
EM: Round [47] log likelihood: -6401.178795
EM: Round [48] log likelihood: -6401.173441
EM: Round [49] log likelihood: -6401.168269
EM: Round [50] log likelihood: -6401.163268
EM: Round [51] log likelihood: -6401.158428
EM: Round [52] log likelihood: -6401.153739
EM: Round [53] log likelihood: -6401.149192
EM: Round [54] log likelihood: -6401.144779
EM: Round [55] log likelihood: -6401.140494
EM: Round [56] log likelihood: -6401.136330
EM: Round [57] log likelihood: -6401.132282
EM: Round [58] log likelihood: -6401.128342
EM: Round [59] log likelihood: -6401.124508
EM: Round [60] log likelihood: -6401.120773
EM: Round [61] log likelihood: -6401.117133
EM: Round [62] log likelihood: -6401.113585
EM: Round [63] log likelihood: -6401.110125
EM: Round [64] log likelihood: -6401.106748
EM: Round [65] log likelihood: -6401.103452
EM: Round [66] log likelihood: -6401.100233
EM: Round [67] log likelihood: -6401.097089
EM: Round [68] log likelihood: -6401.094016
EM: Round [69] log likelihood: -6401.091013
EM: Round [70] log likelihood: -6401.088075
EM: Round [71] log likelihood: -6401.085201
EM: Round [72] log likelihood: -6401.082389
EM: Round [73] log likelihood: -6401.079637
EM: Round [74] log likelihood: -6401.076941
EM: Round [75] log likelihood: -6401.074301
EM: Round [76] log likelihood: -6401.071714
EM: Round [77] log likelihood: -6401.069179
EM: Round [78] log likelihood: -6401.066694
EM: Round [79] log likelihood: -6401.064256
EM: Round [80] log likelihood: -6401.061866
EM: Round [81] log likelihood: -6401.059520
EM: Round [82] log likelihood: -6401.057218
EM: Round [83] log likelihood: -6401.054958
EM: Round [84] log likelihood: -6401.052739
EM: Round [85] log likelihood: -6401.050560
EM: Round [86] log likelihood: -6401.048419
EM: Round [87] log likelihood: -6401.046315
EM: Round [88] log likelihood: -6401.044246
EM: Round [89] log likelihood: -6401.042213
EM: Round [90] log likelihood: -6401.040214
EM: Round [91] log likelihood: -6401.038248
EM: Round [92] log likelihood: -6401.036313
EM: Round [93] log likelihood: -6401.034409
EM: Round [94] log likelihood: -6401.032536
EM: Round [95] log likelihood: -6401.030691
EM: Round [96] log likelihood: -6401.028875
EM: Round [97] log likelihood: -6401.027087
EM: Round [98] log likelihood: -6401.025325
EM: Round [99] log likelihood: -6401.023589
EM: Round [100] log likelihood: -6401.021879
EM: Round [101] log likelihood: -6401.020193
EM: Round [102] log likelihood: -6401.018532
EM: Round [103] log likelihood: -6401.016893
EM: Round [104] log likelihood: -6401.015278
EM: Round [105] log likelihood: -6401.013684
EM: Round [106] log likelihood: -6401.012113
EM: Round [107] log likelihood: -6401.010562
EM: Round [108] log likelihood: -6401.009031
EM: Round [109] log likelihood: -6401.007521
EM: Round [110] log likelihood: -6401.006030
EM: Round [111] log likelihood: -6401.004558
EM: Round [112] log likelihood: -6401.003105
EM: Round [113] log likelihood: -6401.001670
EM: Round [114] log likelihood: -6401.000253
EM: Round [115] log likelihood: -6400.998853
EM: Round [116] log likelihood: -6400.997470
EM: Round [117] log likelihood: -6400.996103
EM: Round [118] log likelihood: -6400.994752
EM: Round [119] log likelihood: -6400.993418
EM: Round [120] log likelihood: -6400.992098
EM: Round [121] log likelihood: -6400.990794
EM: Round [122] log likelihood: -6400.989505
EM: Round [123] log likelihood: -6400.988230
EM: Round [124] log likelihood: -6400.986969
EM: Round [125] log likelihood: -6400.985722
EM: Round [126] log likelihood: -6400.984489
EM: Round [127] log likelihood: -6400.983269
EM: Round [128] log likelihood: -6400.982062
EM: Round [129] log likelihood: -6400.980868
EM: Round [130] log likelihood: -6400.979687
EM: Round [131] log likelihood: -6400.978517
EM: Round [132] log likelihood: -6400.977360
EM: Round [133] log likelihood: -6400.976215
EM: Round [134] log likelihood: -6400.975081
EM: Round [135] log likelihood: -6400.973959
EM: Round [136] log likelihood: -6400.972848
EM: Round [137] log likelihood: -6400.971748
EM: Round [138] log likelihood: -6400.970659
EM: Round [139] log likelihood: -6400.969580
EM: Round [140] log likelihood: -6400.968512
EM: Round [141] log likelihood: -6400.967454
EM: Round [142] log likelihood: -6400.966406
EM: Round [143] log likelihood: -6400.965369
EM: Round [144] log likelihood: -6400.964340
EM: Round [145] log likelihood: -6400.963322
EM: Round [146] log likelihood: -6400.962313
EM: Round [147] log likelihood: -6400.961313
EM: Round [148] log likelihood: -6400.960323
EM: Round [149] log likelihood: -6400.959342
EM: Round [150] log likelihood: -6400.958369
EM: Round [151] log likelihood: -6400.957405
EM: Round [152] log likelihood: -6400.956450
EM: Round [153] log likelihood: -6400.955503
EM: Round [154] log likelihood: -6400.954565
EM: Round [155] log likelihood: -6400.953635
EM: Round [156] log likelihood: -6400.952713
EM: Round [157] log likelihood: -6400.951799
EM: Round [158] log likelihood: -6400.950894
EM: Round [159] log likelihood: -6400.949995
EM: Round [160] log likelihood: -6400.949105
EM: Round [161] log likelihood: -6400.948222
EM: Round [162] log likelihood: -6400.947347
EM: Round [163] log likelihood: -6400.946479
EM: Round [164] log likelihood: -6400.945618
EM: Round [165] log likelihood: -6400.944765
EM: Round [166] log likelihood: -6400.943919
EM: Round [167] log likelihood: -6400.943080
EM: Round [168] log likelihood: -6400.942247
EM: Round [169] log likelihood: -6400.941422
EM: Round [170] log likelihood: -6400.940604
EM: Round [171] log likelihood: -6400.939792
EM: Round [172] log likelihood: -6400.938986
EM: Round [173] log likelihood: -6400.938188
EM: Round [174] log likelihood: -6400.937395
EM: Round [175] log likelihood: -6400.936610
EM: Round [176] log likelihood: -6400.935830
EM: Round [177] log likelihood: -6400.935057
EM: Round [178] log likelihood: -6400.934290
EM: Round [179] log likelihood: -6400.933529
EM: Round [180] log likelihood: -6400.932774
EM: Round [181] log likelihood: -6400.932025
EM: Round [182] log likelihood: -6400.931281
EM: Round [183] log likelihood: -6400.930544
EM: Round [184] log likelihood: -6400.929813
EM: Round [185] log likelihood: -6400.929087
EM: Round [186] log likelihood: -6400.928367
EM: Round [187] log likelihood: -6400.927652
EM: Round [188] log likelihood: -6400.926944
EM: Round [189] log likelihood: -6400.926240
EM: Round [190] log likelihood: -6400.925542
EM: Round [191] log likelihood: -6400.924849
EM: Round [192] log likelihood: -6400.924162
EM: Round [193] log likelihood: -6400.923480
EM: Round [194] log likelihood: -6400.922803
EM: Round [195] log likelihood: -6400.922132
EM: Round [196] log likelihood: -6400.921465
EM: Round [197] log likelihood: -6400.920804
EM: Round [198] log likelihood: -6400.920147
EM: Round [199] log likelihood: -6400.919496
EM: Round [200] log likelihood: -6400.918849
EM: Round [201] log likelihood: -6400.918208
EM: Round [202] log likelihood: -6400.917571
EM: Round [203] log likelihood: -6400.916939
EM: Round [204] log likelihood: -6400.916311
EM: Round [205] log likelihood: -6400.915689
EM: Round [206] log likelihood: -6400.915071
EM: Round [207] log likelihood: -6400.914458
EM: Round [208] log likelihood: -6400.913849
EM: Round [209] log likelihood: -6400.913245
EM: Round [210] log likelihood: -6400.912645
EM: Round [211] log likelihood: -6400.912050
EM: Round [212] log likelihood: -6400.911459
EM: Round [213] log likelihood: -6400.910872
EM: Round [214] log likelihood: -6400.910290
EM: Round [215] log likelihood: -6400.909712
EM: Round [216] log likelihood: -6400.909139
EM: Round [217] log likelihood: -6400.908569
EM: Round [218] log likelihood: -6400.908004
EM: Round [219] log likelihood: -6400.907443
EM: Round [220] log likelihood: -6400.906886
EM: Round [221] log likelihood: -6400.906333
EM: Round [222] log likelihood: -6400.905784
EM: Round [223] log likelihood: -6400.905239
EM: Round [224] log likelihood: -6400.904698
EM: Round [225] log likelihood: -6400.904162
EM: Round [226] log likelihood: -6400.903629
EM: Round [227] log likelihood: -6400.903099
EM: Round [228] log likelihood: -6400.902574
EM: Round [229] log likelihood: -6400.902053
EM: Round [230] log likelihood: -6400.901535
EM: Round [231] log likelihood: -6400.901021
EM: Round [232] log likelihood: -6400.900511
EM: Round [233] log likelihood: -6400.900004
EM: Round [234] log likelihood: -6400.899501
EM: Round [235] log likelihood: -6400.899002
EM: Round [236] log likelihood: -6400.898506
EM: Round [237] log likelihood: -6400.898014
EM: Round [238] log likelihood: -6400.897526
EM: Round [239] log likelihood: -6400.897041
EM: Round [240] log likelihood: -6400.896559
EM: Round [241] log likelihood: -6400.896081
EM: Round [242] log likelihood: -6400.895606
EM: Round [243] log likelihood: -6400.895135
EM: Round [244] log likelihood: -6400.894667
EM: Round [245] log likelihood: -6400.894202
EM: Round [246] log likelihood: -6400.893741
EM: Round [247] log likelihood: -6400.893283
EM: Round [248] log likelihood: -6400.892829
EM: Round [249] log likelihood: -6400.892377
EM: Round [250] log likelihood: -6400.891929
EM: Round [251] log likelihood: -6400.891484
EM: Round [252] log likelihood: -6400.891042
EM: Round [253] log likelihood: -6400.890603
EM: Round [254] log likelihood: -6400.890168
EM: Round [255] log likelihood: -6400.889735
EM: Round [256] log likelihood: -6400.889306
EM: Round [257] log likelihood: -6400.888879
EM: Round [258] log likelihood: -6400.888456
EM: Round [259] log likelihood: -6400.888035
EM: Round [260] log likelihood: -6400.887618
EM: Round [261] log likelihood: -6400.887204
EM: Round [262] log likelihood: -6400.886792
EM: Round [263] log likelihood: -6400.886383
EM: Round [264] log likelihood: -6400.885978
EM: Round [265] log likelihood: -6400.885575
EM: Round [266] log likelihood: -6400.885175
EM: Round [267] log likelihood: -6400.884778
EM: Round [268] log likelihood: -6400.884383
EM: Round [269] log likelihood: -6400.883992
EM: Round [270] log likelihood: -6400.883603
EM: Round [271] log likelihood: -6400.883217
EM: Round [272] log likelihood: -6400.882833
EM: Round [273] log likelihood: -6400.882452
EM: Round [274] log likelihood: -6400.882074
EM: Round [275] log likelihood: -6400.881699
EM: Round [276] log likelihood: -6400.881326
EM: Round [277] log likelihood: -6400.880956
EM: Round [278] log likelihood: -6400.880588
EM: Round [279] log likelihood: -6400.880223
EM: Round [280] log likelihood: -6400.879861
EM: Round [281] log likelihood: -6400.879501
EM: Round [282] log likelihood: -6400.879144
EM: Round [283] log likelihood: -6400.878789
EM: Round [284] log likelihood: -6400.878436
EM: Round [285] log likelihood: -6400.878087
EM: Round [286] log likelihood: -6400.877739
EM: Round [287] log likelihood: -6400.877394
EM: Round [288] log likelihood: -6400.877051
EM: Round [289] log likelihood: -6400.876711
EM: Round [290] log likelihood: -6400.876373
EM: Round [291] log likelihood: -6400.876038
EM: Round [292] log likelihood: -6400.875705
EM: Round [293] log likelihood: -6400.875374
EM: Round [294] log likelihood: -6400.875045
EM: Round [295] log likelihood: -6400.874719
EM: Round [296] log likelihood: -6400.874395
EM: Round [297] log likelihood: -6400.874073
EM: Round [298] log likelihood: -6400.873753
EM: Round [299] log likelihood: -6400.873436
EM: Round [300] log likelihood: -6400.873121
EM: Round [301] log likelihood: -6400.872808
EM: Round [302] log likelihood: -6400.872497
EM: Round [303] log likelihood: -6400.872189
EM: Round [304] log likelihood: -6400.871882
EM: Round [305] log likelihood: -6400.871578
EM: Round [306] log likelihood: -6400.871276
EM: Round [307] log likelihood: -6400.870976
EM: Round [308] log likelihood: -6400.870678
EM: Round [309] log likelihood: -6400.870382
EM: Round [310] log likelihood: -6400.870088
EM: Round [311] log likelihood: -6400.869796
EM: Round [312] log likelihood: -6400.869506
EM: Round [313] log likelihood: -6400.869218
EM: Round [314] log likelihood: -6400.868932
EM: Round [315] log likelihood: -6400.868649
EM: Round [316] log likelihood: -6400.868367
EM: Round [317] log likelihood: -6400.868087
EM: Round [318] log likelihood: -6400.867809
EM: Round [319] log likelihood: -6400.867532
EM: Round [320] log likelihood: -6400.867258
EM: Round [321] log likelihood: -6400.866986
EM: Round [322] log likelihood: -6400.866715
EM: Round [323] log likelihood: -6400.866447
EM: Round [324] log likelihood: -6400.866180
EM: Round [325] log likelihood: -6400.865915
EM: Round [326] log likelihood: -6400.865652
EM: Round [327] log likelihood: -6400.865391
EM: Round [328] log likelihood: -6400.865131
EM: Round [329] log likelihood: -6400.864874
EM: Round [330] log likelihood: -6400.864618
EM: Round [331] log likelihood: -6400.864364
EM: Round [332] log likelihood: -6400.864111
EM: Round [333] log likelihood: -6400.863861
EM: Round [334] log likelihood: -6400.863612
EM: Round [335] log likelihood: -6400.863364
EM: Round [336] log likelihood: -6400.863119
EM: Round [337] log likelihood: -6400.862875
EM: Round [338] log likelihood: -6400.862633
EM: Round [339] log likelihood: -6400.862392
EM: Round [340] log likelihood: -6400.862153
EM: Round [341] log likelihood: -6400.861916
EM: Round [342] log likelihood: -6400.861681
EM: Round [343] log likelihood: -6400.861447
EM: Round [344] log likelihood: -6400.861214
EM: Round [345] log likelihood: -6400.860984
EM: Round [346] log likelihood: -6400.860754
EM: Round [347] log likelihood: -6400.860527
EM: Round [348] log likelihood: -6400.860301
EM: Round [349] log likelihood: -6400.860076
EM: Round [350] log likelihood: -6400.859853
EM: Round [351] log likelihood: -6400.859632
EM: Round [352] log likelihood: -6400.859412
EM: Round [353] log likelihood: -6400.859193
EM: Round [354] log likelihood: -6400.858976
EM: Round [355] log likelihood: -6400.858761
EM: Round [356] log likelihood: -6400.858547
EM: Round [357] log likelihood: -6400.858334
EM: Round [358] log likelihood: -6400.858123
EM: Round [359] log likelihood: -6400.857914
EM: Round [360] log likelihood: -6400.857706
EM: Round [361] log likelihood: -6400.857499
EM: Round [362] log likelihood: -6400.857293
EM: Round [363] log likelihood: -6400.857089
EM: Round [364] log likelihood: -6400.856887
EM: Round [365] log likelihood: -6400.856686
EM: Round [366] log likelihood: -6400.856486
EM: Round [367] log likelihood: -6400.856287
EM: Round [368] log likelihood: -6400.856090
EM: Round [369] log likelihood: -6400.855895
EM: Round [370] log likelihood: -6400.855700
EM: Round [371] log likelihood: -6400.855507
EM: Round [372] log likelihood: -6400.855315
EM: Round [373] log likelihood: -6400.855125
EM: Round [374] log likelihood: -6400.854936
EM: Round [375] log likelihood: -6400.854748
EM: Round [376] log likelihood: -6400.854561
EM: Round [377] log likelihood: -6400.854376
EM: Round [378] log likelihood: -6400.854192
EM: Round [379] log likelihood: -6400.854009
EM: Round [380] log likelihood: -6400.853827
EM: Round [381] log likelihood: -6400.853647
EM: Round [382] log likelihood: -6400.853468
EM: Round [383] log likelihood: -6400.853290
EM: Round [384] log likelihood: -6400.853113
EM: Round [385] log likelihood: -6400.852938
EM: Round [386] log likelihood: -6400.852764
EM: Round [387] log likelihood: -6400.852590
EM: Round [388] log likelihood: -6400.852418
EM: Round [389] log likelihood: -6400.852248
EM: Round [390] log likelihood: -6400.852078
EM: Round [391] log likelihood: -6400.851910
EM: Round [392] log likelihood: -6400.851742
EM: Round [393] log likelihood: -6400.851576
EM: Round [394] log likelihood: -6400.851411
EM: Round [395] log likelihood: -6400.851247
EM: Round [396] log likelihood: -6400.851084
EM: Round [397] log likelihood: -6400.850923
EM: Round [398] log likelihood: -6400.850762
EM: Round [399] log likelihood: -6400.850603
EM: Round [400] log likelihood: -6400.850444
EM: Round [401] log likelihood: -6400.850287
EM: Round [402] log likelihood: -6400.850130
EM: Round [403] log likelihood: -6400.849975
EM: Round [404] log likelihood: -6400.849821
EM: Round [405] log likelihood: -6400.849668
EM: Round [406] log likelihood: -6400.849516
EM: Round [407] log likelihood: -6400.849365
EM: Round [408] log likelihood: -6400.849215
EM: Round [409] log likelihood: -6400.849066
EM: Round [410] log likelihood: -6400.848918
EM: Round [411] log likelihood: -6400.848771
EM: Round [412] log likelihood: -6400.848625
EM: Round [413] log likelihood: -6400.848479
EM: Round [414] log likelihood: -6400.848335
EM: Round [415] log likelihood: -6400.848192
EM: Round [416] log likelihood: -6400.848050
EM: Round [417] log likelihood: -6400.847909
EM: Round [418] log likelihood: -6400.847769
EM: Round [419] log likelihood: -6400.847630
EM: Round [420] log likelihood: -6400.847491
EM: Round [421] log likelihood: -6400.847354
EM: Round [422] log likelihood: -6400.847217
EM: Round [423] log likelihood: -6400.847082
EM: Round [424] log likelihood: -6400.846947
EM: Round [425] log likelihood: -6400.846814
EM: Round [426] log likelihood: -6400.846681
EM: Round [427] log likelihood: -6400.846549
EM: Round [428] log likelihood: -6400.846418
EM: Round [429] log likelihood: -6400.846288
EM: Round [430] log likelihood: -6400.846159
EM: Round [431] log likelihood: -6400.846030
EM: Round [432] log likelihood: -6400.845903
EM: Round [433] log likelihood: -6400.845776
EM: Round [434] log likelihood: -6400.845650
EM: Round [435] log likelihood: -6400.845525
EM: Round [436] log likelihood: -6400.845401
EM: Round [437] log likelihood: -6400.845278
EM: Round [438] log likelihood: -6400.845155
EM: Round [439] log likelihood: -6400.845034
EM: Round [440] log likelihood: -6400.844913
EM: Round [441] log likelihood: -6400.844793
EM: Round [442] log likelihood: -6400.844674
EM: Round [443] log likelihood: -6400.844556
EM: Round [444] log likelihood: -6400.844438
EM: Round [445] log likelihood: -6400.844321
EM: Round [446] log likelihood: -6400.844205
EM: Round [447] log likelihood: -6400.844090
EM: Round [448] log likelihood: -6400.843976
EM: Round [449] log likelihood: -6400.843862
EM: Round [450] log likelihood: -6400.843749
EM: Round [451] log likelihood: -6400.843637
EM: Round [452] log likelihood: -6400.843526
EM: Round [453] log likelihood: -6400.843415
EM: Round [454] log likelihood: -6400.843305
EM: Round [455] log likelihood: -6400.843196
EM: Round [456] log likelihood: -6400.843088
EM: Round [457] log likelihood: -6400.842980
EM: Round [458] log likelihood: -6400.842873
EM: Round [459] log likelihood: -6400.842767
EM: Round [460] log likelihood: -6400.842661
EM: Round [461] log likelihood: -6400.842556
EM: Round [462] log likelihood: -6400.842452
EM: Round [463] log likelihood: -6400.842349
EM: Round [464] log likelihood: -6400.842246
EM: Round [465] log likelihood: -6400.842144
EM: Round [466] log likelihood: -6400.842043
EM: Round [467] log likelihood: -6400.841942
EM: Round [468] log likelihood: -6400.841842
EM: Stopping iterations at round 468 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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam || : 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/tih_rna_sample_00701_B23MVV7LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.Pfam.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.seqsimilar.gff3 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa > /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.49np787MMv/fi_workdir/tih_rna_sample_00701_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir
-done, see /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -5256.767434
EM: Round [1] log likelihood: -5242.972576
EM: Round [2] log likelihood: -5241.329231
EM: Round [3] log likelihood: -5241.187594
EM: Round [4] log likelihood: -5241.173065
EM: Round [5] log likelihood: -5241.166429
EM: Round [6] log likelihood: -5241.160300
EM: Round [7] log likelihood: -5241.154270
EM: Round [8] log likelihood: -5241.148317
EM: Round [9] log likelihood: -5241.142439
EM: Round [10] log likelihood: -5241.136633
EM: Round [11] log likelihood: -5241.130899
EM: Round [12] log likelihood: -5241.125235
EM: Round [13] log likelihood: -5241.119641
EM: Round [14] log likelihood: -5241.114114
EM: Round [15] log likelihood: -5241.108654
EM: Round [16] log likelihood: -5241.103260
EM: Round [17] log likelihood: -5241.097930
EM: Round [18] log likelihood: -5241.092663
EM: Round [19] log likelihood: -5241.087458
EM: Round [20] log likelihood: -5241.082315
EM: Round [21] log likelihood: -5241.077231
EM: Round [22] log likelihood: -5241.072207
EM: Round [23] log likelihood: -5241.067241
EM: Round [24] log likelihood: -5241.062332
EM: Round [25] log likelihood: -5241.057479
EM: Round [26] log likelihood: -5241.052682
EM: Round [27] log likelihood: -5241.047939
EM: Round [28] log likelihood: -5241.043250
EM: Round [29] log likelihood: -5241.038613
EM: Round [30] log likelihood: -5241.034029
EM: Round [31] log likelihood: -5241.029495
EM: Round [32] log likelihood: -5241.025012
EM: Round [33] log likelihood: -5241.020578
EM: Round [34] log likelihood: -5241.016193
EM: Round [35] log likelihood: -5241.011856
EM: Round [36] log likelihood: -5241.007566
EM: Round [37] log likelihood: -5241.003323
EM: Round [38] log likelihood: -5240.999126
EM: Round [39] log likelihood: -5240.994973
EM: Round [40] log likelihood: -5240.990866
EM: Round [41] log likelihood: -5240.986802
EM: Round [42] log likelihood: -5240.982781
EM: Round [43] log likelihood: -5240.978803
EM: Round [44] log likelihood: -5240.974867
EM: Round [45] log likelihood: -5240.970972
EM: Round [46] log likelihood: -5240.967118
EM: Round [47] log likelihood: -5240.963304
EM: Round [48] log likelihood: -5240.959530
EM: Round [49] log likelihood: -5240.955794
EM: Round [50] log likelihood: -5240.952098
EM: Round [51] log likelihood: -5240.948439
EM: Round [52] log likelihood: -5240.944818
EM: Round [53] log likelihood: -5240.941233
EM: Round [54] log likelihood: -5240.937685
EM: Round [55] log likelihood: -5240.934173
EM: Round [56] log likelihood: -5240.930696
EM: Round [57] log likelihood: -5240.927255
EM: Round [58] log likelihood: -5240.923847
EM: Round [59] log likelihood: -5240.920474
EM: Round [60] log likelihood: -5240.917135
EM: Round [61] log likelihood: -5240.913828
EM: Round [62] log likelihood: -5240.910554
EM: Round [63] log likelihood: -5240.907313
EM: Round [64] log likelihood: -5240.904103
EM: Round [65] log likelihood: -5240.900925
EM: Round [66] log likelihood: -5240.897777
EM: Round [67] log likelihood: -5240.894661
EM: Round [68] log likelihood: -5240.891574
EM: Round [69] log likelihood: -5240.888518
EM: Round [70] log likelihood: -5240.885490
EM: Round [71] log likelihood: -5240.882492
EM: Round [72] log likelihood: -5240.879523
EM: Round [73] log likelihood: -5240.876582
EM: Round [74] log likelihood: -5240.873669
EM: Round [75] log likelihood: -5240.870784
EM: Round [76] log likelihood: -5240.867926
EM: Round [77] log likelihood: -5240.865095
EM: Round [78] log likelihood: -5240.862291
EM: Round [79] log likelihood: -5240.859513
EM: Round [80] log likelihood: -5240.856761
EM: Round [81] log likelihood: -5240.854035
EM: Round [82] log likelihood: -5240.851334
EM: Round [83] log likelihood: -5240.848658
EM: Round [84] log likelihood: -5240.846007
EM: Round [85] log likelihood: -5240.843381
EM: Round [86] log likelihood: -5240.840778
EM: Round [87] log likelihood: -5240.838200
EM: Round [88] log likelihood: -5240.835645
EM: Round [89] log likelihood: -5240.833114
EM: Round [90] log likelihood: -5240.830606
EM: Round [91] log likelihood: -5240.828120
EM: Round [92] log likelihood: -5240.825657
EM: Round [93] log likelihood: -5240.823217
EM: Round [94] log likelihood: -5240.820798
EM: Round [95] log likelihood: -5240.818402
EM: Round [96] log likelihood: -5240.816026
EM: Round [97] log likelihood: -5240.813673
EM: Round [98] log likelihood: -5240.811340
EM: Round [99] log likelihood: -5240.809028
EM: Round [100] log likelihood: -5240.806736
EM: Round [101] log likelihood: -5240.804465
EM: Round [102] log likelihood: -5240.802214
EM: Round [103] log likelihood: -5240.799983
EM: Round [104] log likelihood: -5240.797772
EM: Round [105] log likelihood: -5240.795580
EM: Round [106] log likelihood: -5240.793408
EM: Round [107] log likelihood: -5240.791254
EM: Round [108] log likelihood: -5240.789120
EM: Round [109] log likelihood: -5240.787004
EM: Round [110] log likelihood: -5240.784906
EM: Round [111] log likelihood: -5240.782827
EM: Round [112] log likelihood: -5240.780765
EM: Round [113] log likelihood: -5240.778722
EM: Round [114] log likelihood: -5240.776696
EM: Round [115] log likelihood: -5240.774688
EM: Round [116] log likelihood: -5240.772697
EM: Round [117] log likelihood: -5240.770723
EM: Round [118] log likelihood: -5240.768766
EM: Round [119] log likelihood: -5240.766826
EM: Round [120] log likelihood: -5240.764902
EM: Round [121] log likelihood: -5240.762995
EM: Round [122] log likelihood: -5240.761103
EM: Round [123] log likelihood: -5240.759228
EM: Round [124] log likelihood: -5240.757369
EM: Round [125] log likelihood: -5240.755526
EM: Round [126] log likelihood: -5240.753698
EM: Round [127] log likelihood: -5240.751886
EM: Round [128] log likelihood: -5240.750088
EM: Round [129] log likelihood: -5240.748306
EM: Round [130] log likelihood: -5240.746539
EM: Round [131] log likelihood: -5240.744787
EM: Round [132] log likelihood: -5240.743049
EM: Round [133] log likelihood: -5240.741326
EM: Round [134] log likelihood: -5240.739617
EM: Round [135] log likelihood: -5240.737922
EM: Round [136] log likelihood: -5240.736242
EM: Round [137] log likelihood: -5240.734575
EM: Round [138] log likelihood: -5240.732922
EM: Round [139] log likelihood: -5240.731283
EM: Round [140] log likelihood: -5240.729657
EM: Round [141] log likelihood: -5240.728045
EM: Round [142] log likelihood: -5240.726446
EM: Round [143] log likelihood: -5240.724860
EM: Round [144] log likelihood: -5240.723287
EM: Round [145] log likelihood: -5240.721727
EM: Round [146] log likelihood: -5240.720179
EM: Round [147] log likelihood: -5240.718644
EM: Round [148] log likelihood: -5240.717122
EM: Round [149] log likelihood: -5240.715612
EM: Round [150] log likelihood: -5240.714114
EM: Round [151] log likelihood: -5240.712629
EM: Round [152] log likelihood: -5240.711155
EM: Round [153] log likelihood: -5240.709694
EM: Round [154] log likelihood: -5240.708244
EM: Round [155] log likelihood: -5240.706806
EM: Round [156] log likelihood: -5240.705379
EM: Round [157] log likelihood: -5240.703964
EM: Round [158] log likelihood: -5240.702560
EM: Round [159] log likelihood: -5240.701168
EM: Round [160] log likelihood: -5240.699786
EM: Round [161] log likelihood: -5240.698416
EM: Round [162] log likelihood: -5240.697057
EM: Round [163] log likelihood: -5240.695708
EM: Round [164] log likelihood: -5240.694370
EM: Round [165] log likelihood: -5240.693043
EM: Round [166] log likelihood: -5240.691726
EM: Round [167] log likelihood: -5240.690420
EM: Round [168] log likelihood: -5240.689124
EM: Round [169] log likelihood: -5240.687838
EM: Round [170] log likelihood: -5240.686563
EM: Round [171] log likelihood: -5240.685297
EM: Round [172] log likelihood: -5240.684042
EM: Round [173] log likelihood: -5240.682796
EM: Round [174] log likelihood: -5240.681560
EM: Round [175] log likelihood: -5240.680334
EM: Round [176] log likelihood: -5240.679118
EM: Round [177] log likelihood: -5240.677911
EM: Round [178] log likelihood: -5240.676713
EM: Round [179] log likelihood: -5240.675525
EM: Round [180] log likelihood: -5240.674346
EM: Round [181] log likelihood: -5240.673176
EM: Round [182] log likelihood: -5240.672015
EM: Round [183] log likelihood: -5240.670864
EM: Round [184] log likelihood: -5240.669721
EM: Round [185] log likelihood: -5240.668587
EM: Round [186] log likelihood: -5240.667462
EM: Round [187] log likelihood: -5240.666346
EM: Round [188] log likelihood: -5240.665238
EM: Round [189] log likelihood: -5240.664139
EM: Round [190] log likelihood: -5240.663048
EM: Round [191] log likelihood: -5240.661966
EM: Round [192] log likelihood: -5240.660891
EM: Round [193] log likelihood: -5240.659826
EM: Round [194] log likelihood: -5240.658768
EM: Round [195] log likelihood: -5240.657719
EM: Round [196] log likelihood: -5240.656677
EM: Round [197] log likelihood: -5240.655644
EM: Round [198] log likelihood: -5240.654618
EM: Round [199] log likelihood: -5240.653600
EM: Round [200] log likelihood: -5240.652590
EM: Round [201] log likelihood: -5240.651588
EM: Round [202] log likelihood: -5240.650594
EM: Round [203] log likelihood: -5240.649607
EM: Round [204] log likelihood: -5240.648627
EM: Round [205] log likelihood: -5240.647655
EM: Round [206] log likelihood: -5240.646690
EM: Round [207] log likelihood: -5240.645733
EM: Round [208] log likelihood: -5240.644782
EM: Round [209] log likelihood: -5240.643839
EM: Round [210] log likelihood: -5240.642903
EM: Round [211] log likelihood: -5240.641975
EM: Round [212] log likelihood: -5240.641053
EM: Round [213] log likelihood: -5240.640138
EM: Round [214] log likelihood: -5240.639230
EM: Round [215] log likelihood: -5240.638329
EM: Round [216] log likelihood: -5240.637434
EM: Round [217] log likelihood: -5240.636547
EM: Round [218] log likelihood: -5240.635666
EM: Round [219] log likelihood: -5240.634791
EM: Round [220] log likelihood: -5240.633923
EM: Round [221] log likelihood: -5240.633062
EM: Round [222] log likelihood: -5240.632207
EM: Round [223] log likelihood: -5240.631358
EM: Round [224] log likelihood: -5240.630516
EM: Round [225] log likelihood: -5240.629680
EM: Round [226] log likelihood: -5240.628851
EM: Round [227] log likelihood: -5240.628027
EM: Round [228] log likelihood: -5240.627210
EM: Round [229] log likelihood: -5240.626398
EM: Round [230] log likelihood: -5240.625593
EM: Round [231] log likelihood: -5240.624794
EM: Round [232] log likelihood: -5240.624000
EM: Round [233] log likelihood: -5240.623213
EM: Round [234] log likelihood: -5240.622431
EM: Round [235] log likelihood: -5240.621655
EM: Round [236] log likelihood: -5240.620885
EM: Round [237] log likelihood: -5240.620120
EM: Round [238] log likelihood: -5240.619361
EM: Round [239] log likelihood: -5240.618608
EM: Round [240] log likelihood: -5240.617860
EM: Round [241] log likelihood: -5240.617118
EM: Round [242] log likelihood: -5240.616381
EM: Round [243] log likelihood: -5240.615650
EM: Round [244] log likelihood: -5240.614924
EM: Round [245] log likelihood: -5240.614204
EM: Round [246] log likelihood: -5240.613488
EM: Round [247] log likelihood: -5240.612778
EM: Round [248] log likelihood: -5240.612073
EM: Round [249] log likelihood: -5240.611373
EM: Round [250] log likelihood: -5240.610679
EM: Round [251] log likelihood: -5240.609989
EM: Round [252] log likelihood: -5240.609305
EM: Round [253] log likelihood: -5240.608625
EM: Round [254] log likelihood: -5240.607951
EM: Round [255] log likelihood: -5240.607281
EM: Round [256] log likelihood: -5240.606616
EM: Round [257] log likelihood: -5240.605956
EM: Round [258] log likelihood: -5240.605301
EM: Round [259] log likelihood: -5240.604651
EM: Round [260] log likelihood: -5240.604005
EM: Round [261] log likelihood: -5240.603364
EM: Round [262] log likelihood: -5240.602728
EM: Round [263] log likelihood: -5240.602096
EM: Round [264] log likelihood: -5240.601469
EM: Round [265] log likelihood: -5240.600847
EM: Round [266] log likelihood: -5240.600229
EM: Round [267] log likelihood: -5240.599615
EM: Round [268] log likelihood: -5240.599006
EM: Round [269] log likelihood: -5240.598401
EM: Round [270] log likelihood: -5240.597801
EM: Round [271] log likelihood: -5240.597205
EM: Round [272] log likelihood: -5240.596613
EM: Round [273] log likelihood: -5240.596025
EM: Round [274] log likelihood: -5240.595442
EM: Round [275] log likelihood: -5240.594863
EM: Round [276] log likelihood: -5240.594288
EM: Round [277] log likelihood: -5240.593717
EM: Round [278] log likelihood: -5240.593151
EM: Round [279] log likelihood: -5240.592588
EM: Round [280] log likelihood: -5240.592030
EM: Round [281] log likelihood: -5240.591475
EM: Round [282] log likelihood: -5240.590925
EM: Round [283] log likelihood: -5240.590378
EM: Round [284] log likelihood: -5240.589835
EM: Round [285] log likelihood: -5240.589296
EM: Round [286] log likelihood: -5240.588762
EM: Round [287] log likelihood: -5240.588230
EM: Round [288] log likelihood: -5240.587703
EM: Round [289] log likelihood: -5240.587180
EM: Round [290] log likelihood: -5240.586660
EM: Round [291] log likelihood: -5240.586144
EM: Round [292] log likelihood: -5240.585631
EM: Round [293] log likelihood: -5240.585122
EM: Round [294] log likelihood: -5240.584617
EM: Round [295] log likelihood: -5240.584116
EM: Round [296] log likelihood: -5240.583618
EM: Round [297] log likelihood: -5240.583123
EM: Round [298] log likelihood: -5240.582632
EM: Round [299] log likelihood: -5240.582145
EM: Round [300] log likelihood: -5240.581661
EM: Round [301] log likelihood: -5240.581180
EM: Round [302] log likelihood: -5240.580703
EM: Round [303] log likelihood: -5240.580229
EM: Round [304] log likelihood: -5240.579759
EM: Round [305] log likelihood: -5240.579292
EM: Round [306] log likelihood: -5240.578828
EM: Round [307] log likelihood: -5240.578368
EM: Round [308] log likelihood: -5240.577911
EM: Round [309] log likelihood: -5240.577457
EM: Round [310] log likelihood: -5240.577006
EM: Round [311] log likelihood: -5240.576558
EM: Round [312] log likelihood: -5240.576114
EM: Round [313] log likelihood: -5240.575673
EM: Round [314] log likelihood: -5240.575235
EM: Round [315] log likelihood: -5240.574800
EM: Round [316] log likelihood: -5240.574368
EM: Round [317] log likelihood: -5240.573939
EM: Round [318] log likelihood: -5240.573513
EM: Round [319] log likelihood: -5240.573090
EM: Round [320] log likelihood: -5240.572670
EM: Round [321] log likelihood: -5240.572253
EM: Round [322] log likelihood: -5240.571839
EM: Round [323] log likelihood: -5240.571428
EM: Round [324] log likelihood: -5240.571019
EM: Round [325] log likelihood: -5240.570614
EM: Round [326] log likelihood: -5240.570211
EM: Round [327] log likelihood: -5240.569812
EM: Round [328] log likelihood: -5240.569415
EM: Round [329] log likelihood: -5240.569021
EM: Round [330] log likelihood: -5240.568629
EM: Round [331] log likelihood: -5240.568241
EM: Round [332] log likelihood: -5240.567855
EM: Round [333] log likelihood: -5240.567472
EM: Round [334] log likelihood: -5240.567091
EM: Round [335] log likelihood: -5240.566713
EM: Round [336] log likelihood: -5240.566338
EM: Round [337] log likelihood: -5240.565966
EM: Round [338] log likelihood: -5240.565596
EM: Round [339] log likelihood: -5240.565228
EM: Round [340] log likelihood: -5240.564863
EM: Round [341] log likelihood: -5240.564501
EM: Round [342] log likelihood: -5240.564141
EM: Round [343] log likelihood: -5240.563784
EM: Round [344] log likelihood: -5240.563429
EM: Round [345] log likelihood: -5240.563077
EM: Round [346] log likelihood: -5240.562727
EM: Round [347] log likelihood: -5240.562380
EM: Round [348] log likelihood: -5240.562035
EM: Round [349] log likelihood: -5240.561693
EM: Round [350] log likelihood: -5240.561352
EM: Round [351] log likelihood: -5240.561015
EM: Round [352] log likelihood: -5240.560679
EM: Round [353] log likelihood: -5240.560346
EM: Round [354] log likelihood: -5240.560015
EM: Round [355] log likelihood: -5240.559687
EM: Round [356] log likelihood: -5240.559361
EM: Round [357] log likelihood: -5240.559037
EM: Round [358] log likelihood: -5240.558715
EM: Round [359] log likelihood: -5240.558395
EM: Round [360] log likelihood: -5240.558078
EM: Round [361] log likelihood: -5240.557763
EM: Round [362] log likelihood: -5240.557450
EM: Round [363] log likelihood: -5240.557140
EM: Round [364] log likelihood: -5240.556831
EM: Round [365] log likelihood: -5240.556525
EM: Round [366] log likelihood: -5240.556220
EM: Round [367] log likelihood: -5240.555918
EM: Round [368] log likelihood: -5240.555618
EM: Round [369] log likelihood: -5240.555320
EM: Round [370] log likelihood: -5240.555024
EM: Round [371] log likelihood: -5240.554730
EM: Round [372] log likelihood: -5240.554438
EM: Round [373] log likelihood: -5240.554149
EM: Round [374] log likelihood: -5240.553861
EM: Round [375] log likelihood: -5240.553575
EM: Round [376] log likelihood: -5240.553291
EM: Round [377] log likelihood: -5240.553009
EM: Round [378] log likelihood: -5240.552729
EM: Round [379] log likelihood: -5240.552451
EM: Round [380] log likelihood: -5240.552175
EM: Round [381] log likelihood: -5240.551901
EM: Round [382] log likelihood: -5240.551628
EM: Round [383] log likelihood: -5240.551358
EM: Round [384] log likelihood: -5240.551089
EM: Round [385] log likelihood: -5240.550822
EM: Round [386] log likelihood: -5240.550558
EM: Round [387] log likelihood: -5240.550294
EM: Round [388] log likelihood: -5240.550033
EM: Round [389] log likelihood: -5240.549774
EM: Round [390] log likelihood: -5240.549516
EM: Round [391] log likelihood: -5240.549260
EM: Round [392] log likelihood: -5240.549006
EM: Round [393] log likelihood: -5240.548754
EM: Round [394] log likelihood: -5240.548503
EM: Round [395] log likelihood: -5240.548254
EM: Round [396] log likelihood: -5240.548007
EM: Round [397] log likelihood: -5240.547761
EM: Round [398] log likelihood: -5240.547517
EM: Round [399] log likelihood: -5240.547275
EM: Round [400] log likelihood: -5240.547035
EM: Round [401] log likelihood: -5240.546796
EM: Round [402] log likelihood: -5240.546558
EM: Round [403] log likelihood: -5240.546323
EM: Round [404] log likelihood: -5240.546089
EM: Round [405] log likelihood: -5240.545856
EM: Round [406] log likelihood: -5240.545626
EM: Round [407] log likelihood: -5240.545396
EM: Round [408] log likelihood: -5240.545169
EM: Round [409] log likelihood: -5240.544943
EM: Round [410] log likelihood: -5240.544718
EM: Round [411] log likelihood: -5240.544495
EM: Round [412] log likelihood: -5240.544274
EM: Round [413] log likelihood: -5240.544054
EM: Round [414] log likelihood: -5240.543835
EM: Round [415] log likelihood: -5240.543618
EM: Round [416] log likelihood: -5240.543403
EM: Round [417] log likelihood: -5240.543189
EM: Round [418] log likelihood: -5240.542976
EM: Round [419] log likelihood: -5240.542765
EM: Round [420] log likelihood: -5240.542555
EM: Round [421] log likelihood: -5240.542347
EM: Round [422] log likelihood: -5240.542140
EM: Round [423] log likelihood: -5240.541935
EM: Round [424] log likelihood: -5240.541731
EM: Round [425] log likelihood: -5240.541529
EM: Round [426] log likelihood: -5240.541327
EM: Round [427] log likelihood: -5240.541127
EM: Round [428] log likelihood: -5240.540929
EM: Round [429] log likelihood: -5240.540732
EM: Round [430] log likelihood: -5240.540536
EM: Round [431] log likelihood: -5240.540342
EM: Round [432] log likelihood: -5240.540149
EM: Round [433] log likelihood: -5240.539957
EM: Round [434] log likelihood: -5240.539766
EM: Round [435] log likelihood: -5240.539577
EM: Round [436] log likelihood: -5240.539389
EM: Round [437] log likelihood: -5240.539203
EM: Round [438] log likelihood: -5240.539017
EM: Round [439] log likelihood: -5240.538833
EM: Round [440] log likelihood: -5240.538650
EM: Round [441] log likelihood: -5240.538469
EM: Round [442] log likelihood: -5240.538288
EM: Round [443] log likelihood: -5240.538109
EM: Round [444] log likelihood: -5240.537931
EM: Round [445] log likelihood: -5240.537755
EM: Round [446] log likelihood: -5240.537579
EM: Round [447] log likelihood: -5240.537405
EM: Round [448] log likelihood: -5240.537232
EM: Round [449] log likelihood: -5240.537060
EM: Round [450] log likelihood: -5240.536889
EM: Round [451] log likelihood: -5240.536719
EM: Round [452] log likelihood: -5240.536551
EM: Round [453] log likelihood: -5240.536383
EM: Round [454] log likelihood: -5240.536217
EM: Round [455] log likelihood: -5240.536052
EM: Round [456] log likelihood: -5240.535888
EM: Round [457] log likelihood: -5240.535725
EM: Round [458] log likelihood: -5240.535564
EM: Round [459] log likelihood: -5240.535403
EM: Round [460] log likelihood: -5240.535243
EM: Round [461] log likelihood: -5240.535085
EM: Round [462] log likelihood: -5240.534928
EM: Round [463] log likelihood: -5240.534771
EM: Round [464] log likelihood: -5240.534616
EM: Round [465] log likelihood: -5240.534462
EM: Round [466] log likelihood: -5240.534309
EM: Round [467] log likelihood: -5240.534156
EM: Round [468] log likelihood: -5240.534005
EM: Round [469] log likelihood: -5240.533855
EM: Round [470] log likelihood: -5240.533706
EM: Round [471] log likelihood: -5240.533558
EM: Round [472] log likelihood: -5240.533411
EM: Round [473] log likelihood: -5240.533265
EM: Round [474] log likelihood: -5240.533120
EM: Round [475] log likelihood: -5240.532976
EM: Round [476] log likelihood: -5240.532833
EM: Round [477] log likelihood: -5240.532691
EM: Round [478] log likelihood: -5240.532550
EM: Round [479] log likelihood: -5240.532409
EM: Round [480] log likelihood: -5240.532270
EM: Round [481] log likelihood: -5240.532132
EM: Round [482] log likelihood: -5240.531994
EM: Round [483] log likelihood: -5240.531858
EM: Round [484] log likelihood: -5240.531722
EM: Round [485] log likelihood: -5240.531588
EM: Round [486] log likelihood: -5240.531454
EM: Round [487] log likelihood: -5240.531321
EM: Round [488] log likelihood: -5240.531189
EM: Round [489] log likelihood: -5240.531058
EM: Round [490] log likelihood: -5240.530928
EM: Round [491] log likelihood: -5240.530799
EM: Round [492] log likelihood: -5240.530670
EM: Round [493] log likelihood: -5240.530543
EM: Round [494] log likelihood: -5240.530416
EM: Round [495] log likelihood: -5240.530290
EM: Round [496] log likelihood: -5240.530165
EM: Round [497] log likelihood: -5240.530041
EM: Round [498] log likelihood: -5240.529918
EM: Round [499] log likelihood: -5240.529796
EM: Round [500] log likelihood: -5240.529674
EM: Round [501] log likelihood: -5240.529553
EM: Round [502] log likelihood: -5240.529433
EM: Round [503] log likelihood: -5240.529314
EM: Round [504] log likelihood: -5240.529196
EM: Round [505] log likelihood: -5240.529078
EM: Round [506] log likelihood: -5240.528961
EM: Round [507] log likelihood: -5240.528845
EM: Round [508] log likelihood: -5240.528730
EM: Round [509] log likelihood: -5240.528616
EM: Round [510] log likelihood: -5240.528502
EM: Round [511] log likelihood: -5240.528389
EM: Round [512] log likelihood: -5240.528277
EM: Round [513] log likelihood: -5240.528165
EM: Round [514] log likelihood: -5240.528055
EM: Round [515] log likelihood: -5240.527945
EM: Round [516] log likelihood: -5240.527836
EM: Round [517] log likelihood: -5240.527727
EM: Round [518] log likelihood: -5240.527620
EM: Round [519] log likelihood: -5240.527513
EM: Round [520] log likelihood: -5240.527406
EM: Round [521] log likelihood: -5240.527301
EM: Round [522] log likelihood: -5240.527196
EM: Round [523] log likelihood: -5240.527092
EM: Round [524] log likelihood: -5240.526988
EM: Round [525] log likelihood: -5240.526886
EM: Round [526] log likelihood: -5240.526784
EM: Round [527] log likelihood: -5240.526682
EM: Round [528] log likelihood: -5240.526582
EM: Round [529] log likelihood: -5240.526482
EM: Stopping iterations at round 529 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.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_1.fastp.fastq.gz: 296348474
Execution Time = 5.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa --gtf /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf  > /tmp/nxf.49np787MMv/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.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fa --gtf /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gtf  > /tmp/nxf.49np787MMv/fi_workdir/microH.dat
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.49np787MMv/fi_workdir/microH.dat /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.49np787MMv/fi_workdir/microH.dat /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.49np787MMv --json_outfile /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00701_B23MVV7LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.49np787MMv --json_outfile /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00701_B23MVV7LT4_1
Running: touch /tmp/nxf.49np787MMv/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.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00701_B23MVV7LT4_1 --html_output /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00701_B23MVV7LT4_1 --html_output /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000260126.2]
WARNING, no entry stored in dbm for [ENSG00000254681.6]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000226067.7]
WARNING, no entry stored in dbm for [ENSG00000231424.3]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.49np787MMv/ctat_genome_lib_build_dir > /tmp/nxf.49np787MMv/tih_rna_sample_00701_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.49np787MMv/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory